Sonic Chronicles: Sodor Chaos
by Kingstriker
Summary: First Sonic/Thomas crossover. The Island of Sodor would never be the same when strange mishaps start to happen around the island stretching from robotic doppelgangers invading, to an evil revived black knight rampaging, to even an ancient villain seeking to rebuild his robotic empire. Just when the number one blue tank engine thinks hope is lost, he meets a heroic blue hedgehog.
1. Metal Sonic PT 1

**_Hello everyone, Kingstriker here! And I got to say that I've been wanting to do this for quite awhile. This may be my biggest crossover yet since I have a lot of plans for this. And by plans I mean arcs! There will be quite a few and I will list them down below. I've already mixed Thomas with Transformers like 4 times, but this time it will be Thomas mixed with Sonic. For the villains, they will both be from different continuities but be brought together here and will most likely be out-of-character because it's hard for me to keep a character's personality without veering off to make them do something that wouldn't normally do. Down below are the lists of the Arcs._**

 ** _ARC 1: Blue Metal Discovery_**

 ** _ARC 2:_** ** _Island of Camelot_**

 ** _ARC 3: Wisps of Sodor_**

 ** _ARC 4: Metarex Mayhem_**

 ** _ARC 5: Rise of Lyric_**

 ** _And yes I'm a fan of Sonic Boom, the TV show, games and comics. Plus Lyric is now one of my favorite Sonic villains, especially design wise. Anyways this will cover it. I think each arc will take at least 2 or 3 chapters. Basically in this universe the Island of Sodor is on Mobius. Hope you guys enjoy this crossover. And remember, all the villians will not be in complete character._**

* * *

Sonic Chronicles: Sodor Chaos

ARC 1: Blue Metal Discovery

Chapter 1: Metal Sonic PT 1

What he thought would be an easy night battle would turn into nothing but a common defeat for Metal Sonic. He had long since escaped from Sonic and his friends after he ended up getting overwhelmed. He needed to recharge somewhere where they wouldn't find him. He was badly damaged and his emergency repairs would take awhile. As he flew through the sky he felt his power beginning to fail and he looked down to see some land below, it looked like some kind of island. His thruster finally gave away and he flew down towards the island...which happened to be the Island of Sodor, home to Thomas the tank engine.

The number 1 blue tank engine had just finished taking passengers to Ffarquhar station and was ready to go back to the engine sheds to sleep so he could prepare for a hard day of work tomorrow. As he traveled home, he didn't notice something twinkling in the sky behind him. But Clarabel noticed.

"Annie, I have never seen a star as big as that one before." Clarabel said.

"Really?" Annie asked.

"Yes...in fact it looks like it's smoking and...GETTING CLOSER TO US!"

Annie and Clarabel's eyes went wide as they realized it wasn't just some star.

"THOMAS WATCH OUT!" Annie yelled.

Thomas applied his breaks when the supposed star came crashing to the ground right next to the rails. Thomas shut his eyes as dust rose everywhere.

"Cinders and ashes, what is that?" Thomas asked as the dust started to clear up.

What he saw was some blue robot badly damaged and sparking in a few places. The robot struggled to get up as it clawed the ground. Thomas, Annie and Clarabel were speechless when the robot finally looked up at them. Metal Sonic was actually a little surprised by what he was seeing, a blue engine with a face. Metal Sonic didn't find the engine a threat and grabbed his left arm as it started to spark even more. Despite Thomas not being a threat, he still needed answers.

"Identify yourself." Metal Sonic demanded.

"Uh...I'm Thomas. I assume you are not from around here, this is the Island of Sodor." Thomas told him.

Metal Sonic nodded once as a confirmation. He began to examine his injuries while Thomas watched with curiosity.

"Who are you? And what happened to you?" Thomas asked.

"My name is Metal Sonic. I was on a classified mission...that failed again. I need to recharge somewhere as it is not safe for me to be doing anything until I'm back to 100%." Metal Sonic said.

"Hmm...well maybe you could rest at Tidmouth Sheds, it's where me and my friends sleep. Then hopefully by morning you'll be feeling much better." Thomas said.

Metal Sonic could not trust anyone on this island...yet...he honestly didn't have much of a choice due to his condition. He couldn't fly, nor could he fight Sonic...he was useless. He didn't plan on making friends with anyone, he just needed to repair himself and get off this island and battle Sonic again, hopefully it would be just him next time. But for now, he had no choice but to accept the offer.

"Very well."

Thomas' driver and fireman got out to help Metal Sonic into the cab. Normally Metal Sonic would get angry and attack anyone who touched him, but he allowed them to carry him into the cab and Thomas left back to Tidmouth Sheds. Metal Sonic took the opportunity to look out the windows at the surroundings. There was something...relaxing about this place despite not able to see it in the day. It seemed less chaotic than places he's been whenever he was battling Sonic.

He finally arrived after putting away Annie and Clarabel and slowly backed into his shed. Only a few of the other engines were their sheds. Thomas decided to let Metal Sonic rest and fell asleep too before anyone could talk to him. After the driver and firemen left, Metal Sonic just sat in the cab thinking about future plans. He couldn't stay here forever, but he couldn't defeat Sonic because there were too many on his team. He was no longer affiliated with Dr. Eggman so he was all alone.

 _"Guess I should lay low for awhile."_ Metal Sonic thought before going into recharge.

The next morning, Metal Sonic woke to find this his self-repair was finished and he also noticed most of the engines were missing from the sheds except Thomas and James. He stepped out to find Thomas just waking up.

"Thomas...where is everyone?" Metal Sonic asked.

"Oh they had jobs to do. Sir Topham Hatt hasn't told me to do anything yet." Thomas informed him.

"Is this Sir Topham Hatt your master?" Metal Sonic asked.

Thomas winced a bit knowing that term has never been used...plus it was a bit awkward.

"Um...not exactly. But he's the controller of the railway." Thomas corrected him.

"So...your master..." Metal Sonic tilted his head.

"Uh...well...OOH here he comes now." Thomas smiled.

Just in time to decrease the awkwardness, Sir Topham Hatt pulled up in his car and came out smiling.

"Thomas, I have an important job for you now...who...what is that?" Sir Topham Hatt gasped at the robot.

Metal Sonic didn't hesitate to answer him.

"I am Metal Sonic, created by Dr. Eggman to dest-I MEAN HELP...help out on...heroic missions. I'm currently on a classified mission. I assume you are Sir Topham Hatt." Metal Sonic pointed a claw at him.

"Why yes I am...it's nice to meet you Metal Sonic."

STH went for a handshake and Metal Sonic accepted it though STH thought his hand was very cold.

"Thomas your job is to take the children to the school since Bertie has broken down again. Maybe bring Metal Sonic along with you." STH suggested.

"Yes sir, come on Metal!" Thomas whistled.

"Very well." Metal shrugged.

Metal knew he had to get on everybody's good side if he was gonna be able to stay here to lay low. The driver and fireman were still afraid of him as they didn't look back at Metal who sat in the back of the cab. Metal Sonic wondered if he'd please people faster by helping them, sure the jobs wouldn't be too hard. Thomas collected Annie and Clarabel and set off to find Bertie. Metal Sonic once again watched many engines go by and thought the environment was pretty nice. Whenever he got to go out, it was only to fight Sonic.

"This place really doesn't seem too bad." Metal Sonic whispered to himself.

They eventually find Bertie at Wellsworth Station and Thomas whistled to his friend.

"Hello Bertie, sorry you've broken down again." Thomas said.

"It's okay, thank you for helping me out. And hopefully soon we can have another race!" Bertie said.

"Someday Bertie. HOP ABOARD CHILDREN!" Thomas announced.

Metal Sonic watched as a bunch of children raced into the coaches, he slipped out the cab and decided to sit on top of Thomas' boiler for a better view of the world. As Thomas set off for the school, Metal Sonic just relaxed as the cool wind bashed against his frame. The sun was shining down on his clean armor and actually just felt good. Normally a robot wouldn't have emotions...but like E-123 Omega kinda did...so did Metal. He felt...happy for once.

"I wonder where I could provide some assistance." Metal Sonic rubbed his head.

"If you're looking to help, maybe we could find some of the others and see if they might need it." Thomas suggested.

"Sounds good." Metal nodded.

They arrived at the school and the children raced out towards the buildings talking and laughing. Metal shuttered about what happen if he was trapped in one of the coaches with all of them. Afterwards they stopped by the docks where Salty was busy telling a new story to Cranky who was actually interested. Percy was there getting some flatbeds loaded with some crates being lowered by Cranky.

"Ahoy Thomas, you're just in time for another story!" Salty said.

"I'd love to hear it, what do you think Metal Sonic?" Thomas asked.

Hearing the name, Salty, Cranky and Percy were confused as to who he was talking about.

"Who's Metal Sonic Thomas?" Percy asked.

"I am!"

Metal Sonic made himself known by jumping off Thomas and landing the ground making it shake it bit. The others had not seen such a robot before.

"Whoa...never thought I'd see someone like you before." Cranky said.

"A real sentient robot." Salty gasped.

"What do you do?" Percy asked.

Metal Sonic unfortunately had to lie again. Luckily they all seemed foolish enough to believe him.

"I was programmed by...my master...to assist in helping the world and...working...with the hero known as Sonic the Hedgehog. Currently I'm on a classsified mission." Metal Sonic lied and he hated how he had to use his enemy's name.

"Cool!" Percy smiled.

Metal Sonic saw the crates Cranky was getting and decided to make the job faster. He flew over to the ship and started to carry the last remaining crates over to Percy's flatbed while Cranky was astonished. Some of the workers clapped and cheered. Metal felt proud of himself and went to sit back on Thomas' boiler.

"Nothing to it." Metal shrugged.

"Wow...thanks Metal." Cranky said.

"Yes, nice job in deed." Thomas said.

"And now I'm on my way!" Percy whistled and left.

"So...I believe you had a story to tell." Metal pointed to Salty.

"Indeed matey."

And so Salty told his tale which intrigued Metal. Later Metal and Thomas raced around Sodor looking to find engines to help. When a man missed Gordon's express, Metal carried him to Gordon's cab to get a ride. When Toby derailed from a broken track, Metal lifted him back on the track past the broken piece. When some troublesome trucks were causing trouble for Edward and Henry at the Quarry, Metal was there to threaten them and knock some sense into them. By nighttime, everybody was talking about Metal Sonic who had fallen back to recharge for the night.

"He's very nice." Percy said.

"He's very fast like me." Gordon said.

"And he's very helpful." Henry said.

"It's good to have someone like him on Sodor." Edward said.

Everyone except James knew about him since he hadn't been bothered to meet him.

"Well whatever this robot does, as long as it doesn't ruin my paint!" James scoffed.

"I'm sure HE wouldn't do that James." Emily corrected him to reveal his gender.

"We'll see won't we?" James huffed.

Later that night while the engines were asleep, Metal had woken up to go for a flight. He flew across the island through the clear sky and hummed.

"Now this is a place I could get used to." Metal said.

He tried to find any engines still awake and came across the Dieselworks where the diesels were still up and talking. Diesel 10 was talking the most and Metal hatched a plan.

"These guys should be easy to scare." Metal thought.

He flew into the Dieselworks undetected and started to knock things around.

"Whoa! What was that?" Diesel jumped.

"Something probably just toppled over, nothing to worry about." Den said.

"Yeah what he said." Dart added.

Just then more banging and clattering could be heard all over the building. Something even smashed into the side of Diesel 10 making him move forward. His claw snapped wildly.

"ENOUGH PINCHY! But what's going on?" Diesel 10 said.

A barrel goes flying past Diesel who retreats, then a metal pole and other junk were tossed around towards the diesels who scattered screaming. Diesel 10 caught an old wheel in his claw and threw it down beside him.

"Who's doing this?" Diesel 10 asked no one in particular.

Then he saw it...there was Metal standing by the entrance staring at the diesel with his red glowing eyes.

"AHH! WHO ARE YOU?" Diesel 10 gasped.

Metal said nothing else and flew straight Diesel 10 in a corkscrew formation making Diesel 10 race back to his little shed where the doors closed in on his sides. He struggled to get back in and managed to before Metal could touch him. If Metal mentally laughed and decided to get back to Tidmouth Sheds.

"That was good...very good indeed." Metal said flying away.

He wondered what awaited him tomorrow...and hoped Sonic would not find him there. Little did he know, he was gonna get some unexpected company soon.

 _ **To be continued...**_

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 ** _This turned out pretty good for a start. I'm excited to get onto this, but unfortunately I won't be updating every day since I'm working on other stories. But stayed tuned!_**


	2. Metal Sonic PT 2

Chapter 2: Metal Sonic PT 2

The next day, Sir Topham Hatt arrived to give the engines some more duties, well not all of them. Thomas, Henry and James were left in the sheds and they were both awake.

"Morning James." Thomas greeted.

"Morning Thomas, you plan on showing off that robot again?" James giggled.

"I don't have to, he can go out on his own you know. But he's probably still recharging." Thomas said.

Henry looked at Metal Sonic who was sitting in Thomas' cab.

"Hmm, hey Thomas, don't you think it's strange how his name is Metal Sonic. Almost like he's supposed to be some kind of robotic version of someone." Henry said.

"Yeah I thought it was strange too. But I'm not bothered by it, hopefully soon he can continue that mission...whatever it is." Thomas said.

"What if he's bad Thomas, after all, he doesn't even look friendly." James asked.

"Oh come on, if he was bad, he wouldn't have befriended us." Thomas scoffed.

"Suit yourself, but if you're wrong, Sir Topham Hatt will be very cross." James said.

Thomas looked down in thought, he hoped he could trust Metal.

 _ **Meanwhile at G.U.N. HQ...**_

Shadow and Rouge were talking alone while the GUN agents were talking about the latest mission.

"So the robot got away huh? Why am I not surprised?" Rouge chuckled.

"Hmph, we could've gone after him. But there would be no point, he was bound to go offline anyway." Shadow scoffed.

"Sure, as many times as he's been defeated by Sonic and rebuilt, it would be no surprise if he comes back." Rouge said.

Shadow said nothing and thought about changing the subject when a GUN agent walked towards them.

"Agents Rouge and Shadow, the commander has found a signal on a chaos emerald on an island. You need to take Omega with you." The agent handed Rouge the envelop.

"Hmm, the Island of Sodor huh? Very well, maybe I could find some jewels while I'm there." Rouge said.

Shadow crossed his arms and shook his head with shame. She was never gonna stop was she? Just as Omega came over, Shadow took out his green chaos emerald and chaos controlled them there.

 _ **Back on Sodor...**_

Team Dark arrive by a long stretch of track which was part of the main line. They look around seeing nobody there.

"It's a little quiet...too quiet." Rouge figured.

Omega did a scan of the island.

"This island is equally divided by meatbags and other robotics...sentient robotics...I think I just found what you would call my "Happy Place"." Omega used his claws to air quote the setting.

"Interesting, now to find some valuable stuff." Rouge smirked.

Shadow allowed a small smile to creep onto his face.

"I assume you're gonna ask for help, or search the scrap yard?" Shadow turned his head to her.

"Shut up Shadow, I don't need help to find jewels, In fact I-"

Rouge is cut off when they heard Gordon's whistle, the big blue engine came into view pulling the express. The three were rather surprised to see how sentient the engine was due to it having a face. Gordon didn't seem to notice them as he raced by with 4 express coaches.

"Woah, he's pretty big. You got competition Omega." Rouge looked up at the robot.

Omega clenched his claws into fists and he looked to the sky.

"I shall investigate these inferior robots myself." Omega said.

Before Shadow or Rouge could argue, Omega flew off into the distance.

"Are you sure having Omega go off by himself is a good idea?" Rouge asked.

"No...but we'd cover more ground so we can find the chaos emerald." Shadow decided.

"Fine, just don't get lost." Rouge teased.

Shadow said nothing before skating away. Meanwhile, Percy was out at the quarry helping Mavis sort out some trucks into sidings. The trucks didn't want to be shunted and were giving them a hard time.

"Come on you silly trucks, we have a lot of work to do here." Percy groaned.

"NO! NO! WE DON'T WANT TO!" The trucks argued.

"Ugh." Percy said.

Mavis came over looking exhausted.

"You too huh?" Mavis chuckled.

"Yeah, it's such a bother...but I can manage." Percy assured.

Rouge had flown by and used her Treasure Scope to search for any hidden jewels in the rocks. Using her feet she began to dig through different walls of rocks and found a few large jewels.

"Hmm, these will do. But I'm sure there's more." Rouge looked around.

She spotted Percy and Mavis working and Percy was still struggling with the trucks, they wouldn't budge and the siding was not that far away.

"I guess he's in need of some extra muscle." Rouge thought.

She flew down with her massive strength she kicked the front troublesome truck into the others and they all went straight into the siding and slammed into each other. The trucks were dazed and confused.

"Woah, thanks for your help! Who are you?" Percy asked.

"I'm Rouge the bat, but just call me Rouge. And you are?" Rouge asked landing on her feet.

"I'm Percy, we don't get many mobians around here." Percy said.

It was true that then engines were aware of mobians but none lived on the island. Mavis came over after finally getting her trucks in place.

"Excellent work, I saw the whole thing. So what's a mobian doing around here?" Mavis asked.

"Oh I'm just a treasure hunter looking for some nice jewels to collect, and I've already found a few." Rouge said.

"I bet there are a lot of valuable items around the island." Percy said.

This intrigued Rouge, and while she usually never needed help...it wouldn't hurt to have someone tag along.

"Well then sweetie, would you like to help me?" Rouge smirked.

"Sure, I'm finished with my job. What are you going to do Mavis?" Percy asked.

"I have to rest, but you have fun." Mavis said before leaving.

"Alright, see ya!"

Rouge sat on Percy's deck as Percy whistled and left the quarry to help find more valuable objects. Back with Omega, he flew over the island looking down on all the engines, vehicles and humans working together on their jobs. He felt what others called "Jealous" that there were more robotic being around unlike at Station Square where it was just him and those pathetic GUN robots who he felt were useless. He thought it was strange how the engines actually enjoyed working, yet seemed sad whenever something went wrong. These beings apparently were not fond of destroying like he was.

"These robots are much more confusing than Gamma or any of the robots before me. Where are their weapons? Can they fly? Can they feel pain?"

Omega had all those questions in his head until he noticed Harold the Helicopter flying ahead of him.

"Okay so some can fly...he must be one of the lucky ones." Omega figured.

He finally flew over Tidmouth Sheds thinking it was some kind of base. James had already left leaving Thomas and Henry behind who were back to sleeping. Metal Sonic was just awakening when he saw Omega walking over to Henry. Metal Sonic didn't panic and instead stayed hidden, he knew he would blow his chances if Omega spotted him. If there was one thing Omega would get totally wrong, it would be the number identification. Omega thought that the higher the number, the more superior you were..so to him...Thomas must have been the most powerful since he was #1. But first he awoke Henry who was rather shocked to see the bigger robot in front of him.

"Large green robot, identify yourself." Omega demanded.

"I'm Henry...who are you?" Henry asked.

"I am E-123 Omega, agent of G.U.N., we are looking for a chaos emerald." Omega explained.

"Um...what's a chaos emerald?" Henry asked.

"I do not expect you to know that at all. What I am more interested in is how that little blue robot gained superiority." Omega pointed to the sleeping Thomas.

"Thomas is strong...but he's not the strongest." Henry admitted.

"You're covering for him!" Omega accused Henry.

"What?"

"Thomas is obviously the most powerful, AND I WILL CHALLENGE HIM!" Omega raised his voice.

This woke up Thomas who looked around almost in a panic.

"WHO-WHAT-WHERE...oh you're new!" Thomas said.

"Thomas, I challenge you for title of superior machine!" Omega walked in front of him.

"Um what? What kind of challenge?" Thomas asked.

Omega examined him all over while Metal Sonic had to hide under him. When Omega was finished, he went back in front of him.

"A race!"

Thomas could sense this would be much more difficult than his races with Bertie. He felt very intimidated with the hulking robot towering over him. Metal Sonic had sneaked back into the cab and growled.

"I got to get rid of him." Metal Sonic thought.

"Thomas, he's from G.U.N., you better be very careful." Henry told him.

"Do you accept...Thomas?" Omega asked.

What choice did he have, he figured the robot would do something to him if he refused.

"Okay...but to where?" Thomas asked.

Henry had an idea.

"How about to the quarry? It's a pretty long way from here and it will give you a bit of a fair chance." Henry said.

Omega scanned the island again to find the Quarry and found it.

"Reasonable finish, very well. Let's begin!" Omega said.

Omega gave Thomas a 10 second head start before they raced away from the sheds. Omega flew in the air next to him.

"GO THOMAS!" Henry shouted.

But Omega didn't plan to play very fair, but neither was Metal Sonic. He finally revealed himself by racing up beside Thomas, Omega wasn't that surprised.

"Looks like I'll be showing you both who the better robot is." Omega said.

Metal Sonic's red eyes glowed angrily leaving Thomas unaware that he had just stepped between the robot showdown. With Shadow, he was following the signal to where the chaos emerald was while skating beside the main line. He zipped by a few stations and people who didn't expect to see him. Shadow could care less about anything that was going on around here, he was just worried about finding the emerald. Engines like Edward, Toby and even Donald and Douglas were surprised by the black and red hedgehog.

"Hmm, I must be getting close. The signal is very strong." Shadow said.

At one point he passed by Percy and Rouge who were still collecting jewels. Rouge had just found a few more by the windmill.

"Wow...so many jewels. I'll have to come by here more often." Rouge said.

"That would be nice." Percy smiled.

Rouge smiled back at him, maybe this place wouldn't be so bad to use as a vacation spot. Shadow caught up with Gordon who bragged to himself about how fast he was. But he was silenced when Shadow raced by without a word.

"Whoa...who's that?" Gordon wondered.

Shadow was somehow completely oblivious to Thomas, Omega and Metal Sonic who were still racing nearby. Omega was rather impressed by Thomas' speed, he must have practiced. But Thomas was now conflicted, Omega had tried to explain to Thomas that Metal Sonic was evil, but Metal Sonic tried to say that Omega was the enemy. Seeing the conversation getting nowhere, the robots eventually decided to settle it once and for all, a battle race. Omega transformed his hands into guns and started to shoot at Metal who fired some lazers back. Thomas began to panic.

"Is this really necessary?" Thomas asked.

"YES!" The robots said.

Metal Sonic tried to land a punch to Omega who blocked it and kicked him away. Metal Sonic tried to shoot more lazers but Omega ducked behind Thomas and the lazer shot hit Thomas's side instead.

"OW!" Thomas yelled.

"Sorry." Metal said.

The three raced passed Percy and Rouge who were surprised.

"THOMAS?" Percy gasped.

"So Metal was here all along. Interesting, Percy let's follow them." Rouge said.

"Right!"

Shadow finally found the location of the chaos emerald which was buried within the coal of James' tender. James was on his way to the docks when Shadow jumped straight into his cab startling his driver and fireman. The fireman was just about to shovel some more coal into in the firebox and that pile just happened to have the blue emerald.

"Hand over the emerald." Shadow demanded.

The fireman did so without hesitation before Shadow tried to locate Rouge and Omega.

"Rouge! Come in Rouge, where are you?" Shadow asked.

"Chasing down Omega and Metal Sonic who are racing Thomas." Rouge said.

"Who the hell is-"

Before Shadow could finish, he could see the chase up ahead.

"Nevermind."

Shadow leaped out of the cab and raced ahead surprising James.

"Whoa...things are getting stranger all the time." James thought.

Metal and Omega were busy duking it out right on top of Thomas as if he was an arena. Percy and Rouge had caught up and were trying to assist.

"THOMAS WHAT'S GOING ON?" Percy asked.

"I DON'T KNOW ANYMORE!" Thomas shouted.

Shadow raced up.

"I GOT THE EMERALD!" Shadow held it up.

"Nice work, now what about Omega?" Rouge pointed ahead.

Shadow saw the robots fighting on top of Thomas and decided to join in.

"CHAOS SPEAR!"

Shadow fired some spears at Metal who barely had any time to dodge them. Omega fired at him but missed and ended up destroying the tracks ahead. Seeing no switches up ahead, Shadow had an idea.

"CHAOS CONTROL!"

Everyone is teleported over the broken track and the battle race continues.

"Um Omega, you mind not destroying the island as much as you probably want to?" Rouge groaned.

"ENOUGH!" Omega yelled.

He turned to Thomas.

"Thomas, this isn't over!"

He turned to Metal and tackled him into the sky and the two spiral away far into the distance.

"You engines stay away, we'll finish this." Rouge said.

Thomas and Percy stop while Shadow and Rouge chase after the robots. James arrived looking as horrified as they were.

"Did I just see what I thought I did?" James asked.

"Yep." Thomas and Percy both answered.

The robots continued to battle each other but Metal was simply trying to get away. He needed Thomas to understand, but had to deal with Omega first. They were heading straight for the docks where Cranky was busy unloading some more crates, Metal saw his chance. Metal flew passed Cranky just barely dodging a very large crate he was carrying. But Omega didn't dodge in time.

WHAM!

Omega is smacked by the crate and flung back giving Metal the chance to fly away and escape. Omega crashes into the ground hard damaging more tracks. As he got up, he saw Shadow and Rouge standing there with a disapproving glare. Thomas and Percy arrived.

"Everyone alright?" Thomas asked.

"Where's Metal?" Percy asked.

"We're fine but Metal got away." Rouge said.

"Lucky." Omega grumbled.

"Come on we got what we've came for." Shadow said.

"Wait Shadow." Rouge said.

Rouge walked straight over to Percy and kissed him on the cheek and he blushed.

"Thanks for the jewels, I'll be back for more." Rouge winked.

"And we will finish our challenge Thomas." Omega vowed.

"Hmph...they'll never change. CHAOS CONTROL!" Shadow shouted.

Team Dark leave while Thomas smiles at Percy.

"Again?" Thomas smirked.

"You get used to it." Percy said.

Finally Metal comes back and stands in front of Thomas.

"Thomas...I'm sorry for lying to you. I just needed a place to lay low until Sonic and the others stopped looking for me." Metal said.

But Thomas smiled.

"Evil or not, you were a great help and a good friend." Thomas said.

"You'll come back someday right?" Percy asked.

Metal was mentally happy that Thomas had forgiven him, as for coming back?

"Maybe...if I find the time." Metal said.

"Well...I guess this is goodbye for now." Thomas figured.

"Indeed...and thank you." Metal said.

"For what?" Thomas asked.

"For showing me part of the world."

This made Thomas smile big. Metal nodded once before taking off into the sky leaving the island.

"Farewell Thomas the tank engine...I will see you again...someday..."

 _ **End of ARC 1**_

 _ **To be continued in ARC 2: Island of Camelot...**_

* * *

 _ **So ARC 1 is finished finally. And now for ARC 2, the evil King Arthur is revived and ends up on Sodor...will Sonic and the Knights of the Round Table defeat him once again? Stay tuned!**_


	3. King Arthur PT 1

_**The Railway Series books are featured in this story. I know the books didn't exist in medieval times, but they do here.**_

ARC 2: Island of Camelot

Chapter 3: King Arthur PT 1

A few days have passed since Metal Sonic's departure and things were going back to normal for Thomas and his friends...at least for a short while. The damage Metal and Omega caused had been fixed and the news about it had spread. Thomas continued to wonder if Omega would really come back for another race, though Percy doubted it but Henry figured he would. But Omega was the least of their worries...

 _ **World of Camelot...**_

Ever since Sonic defeated the evil King Arthur and stopped Merlina from destroying the kingdom, the land had became quite peaceful. Since then there had not been any evil monsters trying to take over. Merlina had since been associating with Caliburn and Nimue. And the Knights of the Round Table were still protecting the island with their lives...though they did miss Sonic who was the true King Arthur. But it was awkward to have no orders given to them with Sonic gone. Out of all the knights, Sir Percival missed him the most. She was currently walking down the halls of Castle Camelot thinking about him.

"I hope he's okay." She said quietly.

Having nothing else to do, she went down to where the library was located on the bottom floor of the castle. Inside, she spotted a large table with a few scattered books, someone must have recently been here. One of the books on the table was titled "Sonic and the Black Knight". Remembering the events, she shuttered and didn't dare open it. She heard some chuckling nearby and her ears perked up. Deciding to investigate, she found Gawain and Lancelot reading next to each other at a table.

"Gawain what's so funny?" Percival smirked.

"He's reading a Railway Series book." Lancelot muttered.

"What's wrong with reading a Thomas book? These stories are classics!" Gawain argued.

"Hey guys I found this!" Percival held up the Black Knight book.

"I'd be careful with that." Lancelot warned.

"Yeah, hey I didn't even know the title changed." Gawain took it.

"DON'T OPEN IT!" Lancelot snapped.

"Relax I'm not going to!" Gawain waved him off.

Gawain then went to place it back on the shelve, though not completely in. Percival picked up another Railway Series book called "Thomas the Tank Engine". She smiled when she remembered the days she read these as a kid. Thomas was always her favorite.

"Hmm, if only I could visit there." Percival sighed.

Suddenly, a strange portal began to open up in front of them, the knights brought out their swords.

"What trickery is this?" Gawain shouted.

"Stand your ground." Lancelot said.

But then a familiar blue hedgehog jumped out and the portal closed. There standing in front of the knights was Sonic the Hedgehog.

"Hey guys, long time no see!" Sonic held a thumbs up.

"SIR SONIC!" They shouted and bowed.

"Woah enough of the knight stuff, I just came by to check up on the kingdom. After all I still rule here." Sonic shrugged.

"It's good to see you Sonic...how's everything in your world?" Percival said.

"Going good so far, Eggman hasn't plotted anything so far." Sonic said.

"Egg...man?" Gawain was confused.

"Uh nevermind, but you know what's strange? When I got back to my world, this book was waiting for me where I ended up." Sonic pulled out the book.

It was the same "Sonic and the Black Knight" book the knights just saw. They all gasped.

"What?" Sonic asked.

"We have that same book here...wait...did you open it?" Lancelot asked.

"Of course, plenty of times. Why is something wrong?"

"AHA! TOLD YOU!" Gawain pointed to Lancelot.

"His may not be corrupted, but ours might." Lancelot argued.

"Oh please, what, is that evil King Arthur gonna come back, doubt it. He's slain...it's not possible." Gawain argued back.

"Alright then, if you open it and something does happen, you will do all of my duties until I say so!"

"Alright then."

Everyone braced themselves as Gawain pulled out the book and opened it to a random page...nothing happened.

"See, nothing. You fools were so worried." Gawain laughed.

"WHY IS THIS PLACE A MESS?" Came a yell.

They all jumped when they saw Caliburn standing behind Sonic. The startling caused Gawain to drop the book and it flipped a few pages over and started to shake.

"Uh-oh." Gawain gulped.

"GAWAIN!" Lancelot yelled.

"SORRY!"

Everyone is suddenly tossed back when a large cloud of black smoke shot out of the book. When it settled, standing before them all was a revived King Arthur who was holding his Deathcalibur. Sonic gasped and quickly grabbed Caliburn.

"It's you! But how?" Sonic asked.

"Ha-ha, you fool, some of my energy was hidden away in this book for future use. And now that I'm back, I'LL GET RID OF YOU ONCE AND FOR ALL!" King Arthur said.

"ATTACK SONIC!" Caliburn yelled.

Sonic lunged at King Arthur who blocked his attack with his own sword before kicking the hedgehog away. The Knights of the Round Table proceeded to dish out their own sword swings but King Arthur blocked theirs too!

"Pathetic, you may have defeated me last time, but I don't plan to make the same mistakes." King Arthur growled.

He then used some of his magic to summon his horse from the book and swung his sword one last time to knock Sonic and the knights across the library just as they were about to attack again.

"Now then..."

King Arthur noticed the Railway Series books and saw a picture of the Island of Sodor.

"Hmm...this island may be easy to conquer. I SHALL CLAIM IT FOR MYSELF AS THE NEW CAMELOT!" King Arthur decided.

He used his magic to create a portal onto the current page and with his horse, they jumped right in. Sonic and the knights raced back over just as the portal closed taking the Railway Series book with him.

"NO! HE'S GONE TO THE ISLAND OF SODOR!" Sonic groaned.

"You've been there?" Percival asked.

"No but Shadow told me yesterday when he had to collect a chaos emerald from that place. He said he didn't really care for the place but Rouge did." Sonic said.

"The knights didn't understand a single thing he just said since they weren't familiar with Shadow, Rouge or a chaos emerald making Sonic face-palm.

"Nevermind, now I need to call Tails."

"With that?" Percival pointed to the watch-like device on Sonic's arm.

"Yep. Hey Tails."

 **"Hey Sonic, how is everything?"**

"Not good buddy, the evil King Arthur I told you about got loose on the Island of Sodor. We need to get their now."

 **"Sending a portal for my workshop now!"**

The portal opened back up and Sonic turned to the knights.

"You guys coming?"

"But what about the kingdom?" Gawain asked.

"Aw it will be fine! You ready Caliburn?"

"I'm always ready!" Caliburn smiled.

And so Sonic, Caliburn and the Knights of the Round Table headed to Sonic's world, more specifically Tail's workshop.

 ** _Mobius..._**

The Knights were a amazed by all the tech as they looked around curiously. Tails came running over to Sonic.

"Whoa, so these were the guys you were talking about?" Tails asked.

"Yep. Lancelot who we know as Shadow, Gawain as Knuckles and Percival as Blaze."

"Aren't you supposed to be the Blacksmith?" Lancelot asked.

"The what?"

"Oh yeah you were the smithy in their world." Sonic said.

"Oh...I guess that kinda makes sense. Anyways, we can't take a portal there because the machine needs to recharge, so I just started the Tornado-2, we should get going." Tails said.

"Right come on! Oh wait...how can they all fit?" Sonic asked.

"Uh...well..."

The answer was given in the form of the Knights having to stand on the wings of the plane while Sonic of course got the backseat. The knights didn't seem that fazed by the height or the dangers of doing that. They trusted Tails who promised to fly as steady as he could.

 ** _Island of Sodor..._**

King Arthur flew across the Island examining the place, so far it seemed like the perfect place to conquer. Strangely no one noticed him yet, but was about to make himself noticed.

"These worthless people are no match for me...but these strange sentient machines could be of some use." King Arthur thought.

He looked around as Gordon was pulling the express, Edward was pulling a goods train and Percy was doing some shunting. A little bit of trouble wouldn't hurt. Using the Deathcalibur, he summoned at least 50 of the Knights of the Underworld. He only summoned the Soilder-Ones with spears and swords since they were a lot better in his opinion.

All of you! I want you to help me take over this island, but most importantly...FIND...HIM!"

King Arthur pulled out the Railway Series book and showed them the picture of Thomas on the front cover. The knights bowed before setting off to conquer the island...he was also planning to find Thomas...and turn him into a Knight of the Underworld...

"Now where are you Thomas the Tank Engine...I need to have a word with you...he-he..."

 _ **To be continued...**_

* * *

 _ **Uh-oh...Sonic and the others better get there quick! Will King Arthur's domination of Sodor succeed? Stay tuned!**_


	4. King Arthur PT 2

Chapter 4: King Arthur PT 2

In a matter of minutes, the Knights of the Underworld had started to attack buildings and chase away people...no killing was involved. People hid in their homes and some of the engines began to get derailed. Gordon was halted from pulling the express and some of the knights forced everyone out of the coaches. The knights then knocked the coaches down and pushed Gordon off the rails.

"Hey, that was not necessary. What crazy knights would do this?" Gordon groaned.

The knights said nothing and ran off. Percy was pulling a few trucks down a line when he saw some of the knights slashing the rails.

"Oh no! STOP!" Percy yelled.

He applied his brakes but it was too late. The knights jump back when Percy crashes into the broken track and the trucks fly off the rails laughing and groaning. Percy slides a few feet away from the rails.

"Ugh...who are you guys?" Percy asked.

Again the knights said nothing and instead left. Percy was worried that the island was being taken over, and he no idea how right he was. Even places like the Narrow Gauge railway were getting attacked and taken over. Any engine not in a shed would be pushed off the rails, and those in a shed would be boarded in and trapped. Currently on the Narrow Gauge railway, Duncan was trying his best to outrun 2 knights that were closing in fast. He sped past Skarloey and Rhineas who were already derailed.

"Hurry Duncan!" Rhineas yelled.

"I'm going as fast as I can!" Duncan yelled back.

But as he rounded a bend, 2 more knights were blocking the way.

"Oh rubbish!" Duncan sighed seeing there was no way out.

Back on the other side, the knights had trapped James, Edward and Henry in the sheds. King Arthur was flying around destroying some property and derailing a few engines himself. At the docks, he managed to slice through the bottom of Cranky and knock him down, he destroyed several troublesome trucks and tore into buildings. He even sliced Harold's propellers sending him spiraling down into a field that Trevor and Terrance were working in together.

"Woah Harold, fancy meeting you here!" Trevor said.

"I'm worried about the others. I wonder if Sir Topham Hatt will figure out something." Harold wondered.

"No it's too late. That evil knight has taken over all of Sodor! What can we possible do?" Terrance said.

King Arthur finally arrived at Tidmouth Sheds and looked at the three engines there. He got off his horse and walked in front of them. The knights guarding the engines bowed down.

"Alright you three, I want to know the location of Thomas the tank engine."

"We don't know where he is right now! He could be anywhere running away from your evil knights." Edward said sternly.

"You don't frighten me you metal fools. I'll destroy this whole island, and rebuild it to my specifications. And your friend will help me." King Arthur said.

"Thomas would never join you!" James said.

"Oh but he will when I gain control of him." King Arthur argued back.

He got back to his horse and pointed to the guards.

"GUARDS! KEEP THEM HERE, I'LL SEARCH FOR HIM MYSELF!"

The knights nod while King Arthur flew back into the air and searched for Thomas. Said tank engine had noticed a few of his friends getting derailed and was hoping they would be okay. He raced down the line searching for anyone not derailed.

"Hmm, where would be a good hiding spot?" Thomas wondered.

"Psst, Thomas over here!" He heard a voice.

"Toby? Where are you?" Thomas asked.

He saw a line hidden by some large bushes and could make out a bell. He smiled and went onto the track Toby was on and hid with him.

"Oh thank goodness I found you Toby. What are all these strange knights doing here?" Thomas asked.

"I don't know, but I fear their leader is trying to take over the island. But why here?" Toby asked.

"Who knows, I can't find Annie and Clarabel, but I'm sure they're okay." Thomas figured.

"You better hope so, I heard everyone on the Narrow Gauge railway have been derailed or trapped in sheds. "

"It's best to lay low for awhile here until some help gets here."

The help was closer then they thought, the radar on the Tornado-2 beeped as they were closing in on the island.

"We're approaching the Island of Sodor now!" Tails announced.

"Excellent work Tails, time to teach that fake king a lesson." Sonic said.

"Sonic, do you have a certain plan?" Caliburn asked.

"Uh...not exactly. Um Tails would what would you suggest?" Sonic said.

"I'll drop you guys off in a less populated area and we should split up from there. Cover more ground that way...I'm sure King Arthur will be expecting you." Tails informed him.

"Right!" Sonic held a thumbs up.

Tails lowered some more as they arrived on the island and looked down to see the destruction.

"Oh no, he's already started the rampage. We don't have much time left." Lancelot said.

"I'm ready to throw down with these knights!" Gawain pulled out his swords.

Tails then gave Sonic some more wrist communicators and he then gave them to the knights who were a little surprised by the future technology.

"Use these to communicate with each other, if any of you find King Arthur, let us know and we'll face him together!" Sonic said.

"Yes my lord!" The three bowed.

Sonic mentally groaned and Caliburn chuckled.

"You ready Sonic, we don't know if King Arthur truly is stronger than before, but I doubt he's immortal this time." Caliburn said.

"Hah, we'll take care of him no problem. He just got lucky back in the library because he took us by surprise...but now we're ready for him." Sonic smirked.

"Here's your stop!" Tails said.

Tails hovered over Tidmouth Sheds where they saw the knights trapping James, Henry and Edward.

"Let's do it!" Sonic jumped off.

Taking the knights by surprise, he spin-dashed into one of them knocking it into the others. Then quickly he took Caliburn and slashed them in half and they exploded into puffs of smoke. The engines were surprised to see him and the knights who landed as well.

"I'll search all over the island." Tails yelled.

"You got it Tails!" Sonic said.

"Whoa...are you-"

"Sonic, Sonic the Hedgehog. Nice to meet you guys, and don't worry. Me and the Knights of the Round Table are here to stop King Arthur's reign of terror again." Sonic announced.

"Again?" Henry gasped.

"Yep, it was a long story." Sonic shook his head.

"Sir Sonic, shall we split up now?" Percival asked.

"Yeah, and be careful." Sonic wagged his finger.

The knights nodded and separated while Sonic decided to get more info.

"So I saw some destruction on the way here, what has he been doing?" Sonic asked.

"He's been derailing all of our friends and destroying buildings." Edward informed him.

"We're probably one of the only engines still on rails. He said he was looking for Thomas, but we don't know where he is." James said.

"Hmm, interesting. Well I'll find him, you three stay here!" Sonic then dashed off.

Meanwhile, the Knights of the Round Table started to run into many Knights of the Underworld and began to slay them all. No other people were around besides derailed engines. Lancelot battled a few by the docks and once he was finished there he raced away and found Knapford Station being attacked.

"Hmph, these monsters will never underestimate my power!" Lancelot said before charging into battle.

Gawain was just finishing a small battle at the Quarry and thought it would be funny to release all the coal from a hopper onto some of the knights destroying them instantly. Then he found the Steamworks where Vector and Kevin were trapped in the back while the knights destroyed everything.

"NOT ON MY WATCH YOU CREEPS!" Gawain lunged at a group of knights.

With Percival she was racing down a few tracks passing by some destroyed buildings and broken tracks.

"King Arthur really means it this time. But we won't let him win." Percival promised.

She spotted Tails flying in the air who looked down and waved. Percival waved back and sped up faster.

"Wow...it's hard to believe that these guys look just like-"

"HOLD IT RIGHT THERE!" Came a voice.

Tails slowed down and looked behind him to see King Arthur riding up next to him. Tails had to admit, this knight looked pretty scary.

"Uh, I assume your King Arthur?" Tails asked.

"OF COURSE I AM YOU FOOL! You and that blue menace will never defeat me. NOW SURRENDER!"

King Arthur pulled out the Deathcalibur and swung it at Tails' plane. Tails dodged it and flew off faster but King Arthur chased after him. Constantly Tails had to zip left and right and was trying to find some way to shake him off. King Arthur was closing in on him fast.

"Ugh, these pests really are a thorn in my side. It's time to end this!" King Arthur growled.

As Tails started to go lower to the ground, King Arthur swung a wave of energy and the blast crashes into Tails' plane.

"NO! NOT NOW!"

Tails tries to steer the plan somewhere safe...at least after crashing through a barn. Then he sees Sir Topham Hatt's house up ahead.

"Well...hopefully he's got the money to fix any damage to his house." Tails gulped.

The plane crashes to the ground and slides straight into the side of the fat controller's house. Sir Topham Hatt runs out with his wife in tow as they see Tails on the ground rubbing his head.

"What is going on?" Sir Topham Hatt asked.

"Sorry Sir, my plane crashed after being taken out by King Arthur. His knights are loose all over Sodor!" Tails said.

"Oh I know that, but I don't know what to do!" Sir Topham Hatt sighed.

"Dear we should go back inside, look." Lady Hatt pointed up.

King Arthur came down and pointed his Deathcalibur at Tails and the Hatts.

"Are you the leader of this railway?" King Arthur looked at Sir Topham Hatt.

"Yes I am."

"Well your railway belongs to me now! AND YOU WILL OBEY ME!" King Arthur snarled.

Percival arrived and hid behind some bushes. She contacted Sonic.

"Sonic, I've found King Arthur." Percival whispered.

"Can you give me a sign?" Sonic asked.

Percival pointed her sword in the air and threw up a shot of fire that Sonic, Lancelot and Gawain could see from their spots.

"Got it, we're on our way! Keep him occupied." Sonic said.

"Yes my lord."

Percival then came out of hiding and shot a bit of fire at King Arthur's back.

"WHO DARES HIT ME?" King Arthur turned around.

"I DO! I WILL NOT ALLOW YOU TO TAKEOVER THIS ISLAND!" Percival sneered.

"Hah, you cannot defeat me by yourself! Especially if you failed to defeat Sonic." King Arthur said.

"I'm powerful by myself." Percival pulled out her sword.

"Well then, let's test your might out then."

King Arthur got off his horse who then proceeded to try and attack Tails. The Hatts ran back into the house to avoid harm. Gawain and Lancelot met up by Henry's forest where Thomas and Toby were hiding. Sonic arrived and stopped in front of the knights.

"Come on, we don't have much time!" Sonic said.

"Um, is the coast clear?" They heard a voice.

They saw Thomas and Toby come out of hiding and face them.

"Hey, you guys are still okay." Sonic smiled.

"HOLY CRAP IT'S THOMAS!" Gawain blurted out.

"So you're Thomas, nice to meet you, I'm Sonic the Hedgehog." Sonic introduced himself.

"Nice to meet you too, and this is Toby."

"Hello." Toby rung his bell.

"Are those good knights?" Thomas asked.

"Yep, and Percival is distracting King Arthur as we speak. Maybe you guys can help with the distracting." Sonic said.

Back with Percival she was trying to stand her ground as her sword continued to clash with King Arthur's.

"Give up, you don't have a chance." King Arthur said.

"I wont...give up..." Percival groaned before falling to one knee.

"Hmph, you don't even deserve a scared sword such as that."

"THAT'S WHAT YOU THINK!" Came a voice.

Before King Arthur could turn around, Lancelot and Gawain kicked him in the back of the head and then sonic swept him off his feet.

"Percival are you alright?" Sonic went to help her up.

Once again, Percival blushed.

"Yes I am Sir Sonic, now let's finish him off." Percival gripped her sword tightly.

"Hmph, I'll have your head for this Sonic." King Arthur clenched a clawed fist.

"We'll see about that King Arthur!" Sonic said.

"You will suffer for this destruction." Caliburn said.

The horse tried one more time to hit Tails but as the fox jumped out of the way, Thomas did the unthinkable.

CRASH!

Everyone turned to see that Thomas had ran over the horse's legs, much to King Arthur's horror.

"YOU INFERIOR MACHINE, WHAT HAVE YOU DONE?" King Arthur growled.

Then the horse explodes in a puff of smoke, Toby arrived to get the Hatts away from the area and left quickly.

"Uh-oh." Thomas said.

"YOU WILL PAY FOR THAT YOU LITTLE-"

King Arthur cuts himself off and lunges at Thomas who back away. Sonic and the knights knock King Arthur away and Tails calls to Sonic.

"Sonic, I'll stay behind to fix the plane, you get rid of him!" Tails said.

"YOU GOT IT!' Sonic nodded.

"THOMAS RUN!" Gawain yelled.

Thomas raced off but King Arthur was pretty quick on his feet. He managed to jump and land on top of Thomas.

"YOU WILL BE DESTROYED!" King Arthur growled.

He then stabbed the DeathCalibur into Thomas' left side and sliced a large line into him.

"AHH!" Thomas yelped.

"NO!" Sonic yelled.

The Knights jumped into the cab while Sonic leaped on top of it.

"THIS WILL BE OUR FINAL BATTLE!" Sonic said.

"BRING IT!" King Arthur said.

Like before, Sonic and King Arthur blocked each other blows for a certain period of time before Sonic found an opening and slashed at him a few times before King Arthur knocked him away. Thomas saw a turn up ahead and hoped he could shake the evil knight. But it failed as King Arthur stabbed into Thomas to hold on.

"YOU CAN'T SHAKE ME!" King Arthur said.

"BUT I CAN DESTROY YOU!" Sonic shouted.

The knights tried several times to join in but King Arthur would find time to repel them back. Up ahead were the last remaining groups of the Underworld knights.

"We got this Sir Sonic." Lancelot said.

"Good!" Sonic said.

The nights leaped onto Thomas' front deck and slashed away at the incoming knights. Thomas had an idea, up ahead was Mr. Jolly's Chocolate Factory...though he didn't want to ruin anything else on Sodor, it was for a good cause. Thomas sped up as he got near the factory.

"Sonic, keep him busy I got a plan, when I say NOW, you knock him forward." Thomas said.

"Alright let's see it!" Sonic said blocking another one of King Arthur's blows.

As they came towards the factory, the Knights of the Round Table got a little worried.

"Um Thomas, you sure you know what you're doing?" Gawain asked.

"Ready Sonic? NOW!"

Thomas puts on his brakes and Sonic spin-dashes into King Arthur's face and the evil king flies straight into the side of the factory while Thomas switches tracks and comes to a stop. They listen to the evil king's yells and grunts as the machines inside bash, yank, throw and covered him in fresh chocolate. He crashes through the other side completely battered and beaten and drenched in chocolate. Sonic goes over and pulls up Caliburn.

"I'LL GET YOU ALL FOR THIS ONE DAY!" King Arthur yelled.

"YAH!"

Sonic stabbed King Arthur and he explodes into smoke including his sword.

"Wow...now that's what I call a sticky situation." Sonic joked.

Being from a different reality and not use to jokes, the knights looked confused.

"Ugh nevermind. Great job Thomas...that was a great plan." Sonic said.

"I'm just glad everything worked out. Hey there's Tails." Thomas whistled.

"Sonic is everything alright?" Tails asked landing the fixed plane.

"Yep, he's gone including all the Knights of the Underworld." Sonic said.

"Sir Sonic, thank you for getting rid of him." Percival said.

"Hey I couldn't have done it without you guys!" Sonic smiled at his team.

"So what about the island, there's so much damage." Tails said.

"Well, maybe we could stay and help fix it up." Gawain suggested.

"Hmph, it will take a while." Lancelot said.

"Actually...Sonic...slam my edge down on the ground." Caliburn said.

"Uh..okay."

Sonic slammed down Caliburn's edge and a large wave of energy sweeps across the island...and in seconds...everything is fixed.

"Wow...just like that?" Tails said.

"Yep, so Thomas, we should go check to see how everyone is doing." Caliburn said.

"Alright let's go...are you Knights gonna stay for awhile?" Thomas asked.

"Eh why not? Plus this chocolate is good!" Gawain said scooping some off the ground in his armored hand.

"But we must return soon, our kingdom will need us." Lancelot said.

"Lighten up, just for an hour or 2." Sonic said.

"I'd like to stay for awhile." Percival nodded.

"Well then, let's go exploring!" Sonic said.

Everyone agreed and hopping aboard Thomas as they raced off into the distance.

 _ **END OF ARC 2.**_

 _ **To be continued in ARC 3: Wisps of Sodor...**_

* * *

 _ **Phew, it's been awhile since I updated! But I finally finished this arc, stayed tuned for ARC 3.**_


	5. Wisps PT 1

ARC 3: Wisps of Sodor

Chapter 5: Wisps PT 1

A few days passed since the invasion of King Arthur and the Knights of the Underworld, now things were getting back to normal...again. Sonic, Tails and the Knights of the Round Table had already left and the engines were left to get back to work. Sonic of course had to explain that using Calibrun's power, he managed to restore the island to the way it was. One morning, Gordon was boasting to the engines about how much faster he planned to pull the express that day.

"I plan to go twice as fast this time. And nothing will keep me late." Gordon scoffed.

"Just don't get pushed over this time." James teased.

Gordon rolled his eyes as the engines laughed.

"You didn't get derailed because you, Edward and Henry decided to stay in the sheds, leaving Thomas and Sonic to clear the mess." Gordon argued.

"Those guys looked dangerous, I wasn't going to ruin my paint over that!" James said.

"I ran over that knights' horse and I didn't get hurt!" Thomas piped up.

"That was just luck." James scoffed.

Thomas and Percy looked at each other with annoyed looks, they honestly didn't want to hear a bunch of complaining...nobody else did.

 _ **Planet Wisp...**_

Yacker was planning a little trip with some of his friends where they were going to Mobius to visit Sonic and his friends. Yacker's friends were most of the different types of wisps. There was yellow, cyan, blue, green, pink, purple, orange and a white one like Yacker. They were all eager to go especially Yacker.

"Okay everyone, we need to be careful, I don't want any of you getting lost!" Yacker said.

"Relax, that won't happen!" The pink wisp scoffed.

"You and crazy purple over there always get in trouble." Yacker sneered.

"It's a habit." The purple wisp shrugged.

Yacker face-palmed wondering if he was really doing the right thing. Ever since Sonic and Tails saved their planet and many others from Dr. Eggman, the Wisps had salvaged a few parts of the factory to make a ship in case they wanted to visit Mobius...and now was a good time to use it. Deciding he wasn't going to argue any longer, Yacker ushered them into the ship and he of course was going to pilot it.

As they left the planet, Yacker couldn't help but wonder if this was a good time to visit Sonic, surely there would be time if he wasn't saving the world right now...which he wasn't. He ignored some arguing going on behind him where the purple wisp was picking a fight with the pink one who was daring him to take a swing.

"Will you two knock it off already?" The orange one snarled.

"HE STARTED IT!" The two pointed at each other.

Yacker knew silence would come very soon as he would have to switch to light speed to reach Mobius. When it was time, he proudly hit the button and the wisps started to sink back in their seats from the sudden speed. When it was time to switch back to normal, Yacker looked back at the others.

"How was that?" Yacker asked.

But none of them said anything.

"Thought so."

 _ **Mobius...Island of Sodor...**_

Unknown to the Island of Sodor, another Mobian was on her way to the island. Gordon had arrived at Knapford Station to pick up passengers, one of them was the mobian. She wore black armor all over her body and her helmet had 2 large horns curving backwards like a goat...but it wasn't a goat. She even head a few weapons handy but not needing them right now. As she boarded the express, she sat alone in the back and took off her helmet revealing herself to be the echidna Shade. Ever since Sonic and his friends defeated the Nocturnus Clan and eventually defeated Eggman's new empire, she had decided to go and travel the planet alone. She eventually found the Island of Sodor and figured it would be a place to rest.

"Hmm, this place looks pretty peaceful, though now I'll just have to find some place to sleep." She tapped her chin.

Her thought was interrupted when Gordon blew his whistle.

"EXPRESS COMING THROUGH!" Gordon cheered.

He was trying to go as fast as he said he would and was succeeding so far. Up ahead was Percy who was pulling a few trucks on the track beside Gordon. Percy heard him whistle and come up behind him.

"What did I tell you, I'm going to go faster you've ever seen." Gordon smirked.

"Yeah, you sure did heh." Percy sighed.

Suddenly, a blur of green, purple and gray race by, but they weren't engines.

"Whoa, now they are fast, probably about as fast as Sonic." Percy said.

"Who were they?" Gordon wondered.

Meanwhile on Thomas' branch line, the #1 blue tank engine was racing across the tracks with Annie and Clarabel. He had just got done dropping off some passengers and was just traveling around enjoying the nice weather. Thomas had started to wonder if any more crazy things would happen with Mobians. His thoughts would soon become reality when the 3 mysterious figures from earlier arrive and land on top of Annie.

"Hmph, this place is pretty strange."

"True, but at least there some good treasure to find here, my scanner can detect several items nearby."

"Hey boss, maybe we should split up."

"Good idea Storm...for once."

"He-he."

"Hmm, Wave aren't we on one of those sentient locomotives?"

"I think so Jet."

"Well then, time for me to see if any of these metal-on-wheels can be as fast as me. Too bad Sonic isn't here, I would've tried to prove myself today."

"You'll get your chance, but right now let's look anything valuable."

And so the notorious Babylon Rogues split up, but Jet remained on top of Annie who was wondering why she felt as if someone was on top of her.

"I say, who is on top of me?" Annie said.

"What's going on Annie?" Clarabel asked.

"There's someone standing on me." Annie said.

"I'm the Jet the Hawk, soon-to-be fastest in the universe. All I need to do is beat Sonic the Hedgehog." Jet smirked.

"You know Sonic?" Thomas asked.

Jet flew in front of Thomas and came face-to-face with him.

"Indeed, and who are you?"

"I'm Thomas."

"Well then Thomas, are any of your friends fast?"

"I know Gordon is, he's probably nearby. Though over the years I've proven to be really fast too." Thomas said.

"You? Hah! You don't even look that fast or strong. You'll never be fastest in the universe." Jet teased.

Before Thomas could argue, Jet blasted away in the distance and Thomas rolled his eyes.

"Don't worry Thomas, he'll get what's coming to him." Annie said.

"Indeed." Clarabel agreed.

"I hope you're right." Thomas sighed.

Back with the Wisps, the rocket had finally entered Mobius' atmosphere and Yacker was getting really excited. However, none of the Wisps had even tried to ask Sonic where he most likely would be and knew they would have to land at a random location. They did however look up a map of Mobius and wanted to land somewhere less populated and start from there, after all, a little traveling wouldn't hurt. And so Yacker found the Island of Sodor coordinates and made sure to land there.

As luck would have it, up ahead were Sonic and Tails who were going back to Sodor for a little rest and for Tails to build a small communications tower, after all the stuff that's been happening, the Island needed to stay protected. Tails had planned to build it by Tidmouth Sheds. Yacker tried to get the two to notice but they were far ahead of him. Yacker looked down at the island to see where would be a good place to land but unfortunately he would turn out to be a terrible lander when he picked the Seaside to land.

With a hard crash, the ship hits the sand throwing a lot up and the Wisps are all launched high into the air and into the distance. From above, Sonic and Tails heard the crash.

"What was that?" Sonic asked.

"I don't know, but we better check it out." Tails flew lower.

They arrived by the seaside and found the broken ship. The red metal reminded Sonic of something.

"What is it Sonic?" Tails asked coming over.

"This metal, haven't we seen this before?" Sonic asked.

"It looks like the metal we saw back on Planet Wisp when Eggman tried to take it over."

"Wait...you don't think..."

Sonic put 2 and 2 together and realized the Wisps were here.

"Tails, I have a feeling the Wisps came here and are now in trouble."

"Well we need to find them, maybe Yacker is here too!"

"I miss that little guy, come on, let's go see if any of the engines saw them." They got back in the Tornado-2 and took off to search.

Just as they left, the Babylon Rogues arrived and found the ship. Wave walked over and examined it.

"Hmm, doesn't look that functional anymore, and it's warm. They must have just left." Wave said.

"Well it doesn't matter, it's useless now." Jet came over.

He kicked it, just for the wing to fall on him and Storm and Wave laughed at him.

"IT'S NOT FUNNY!" Jet growled throwing the wing off him.

Storm looked to the sky and spotted Sonic and Tails.

"Hey Boss look!" Storm pointed.

Jet saw his rival and smirked.

"So Sonic really is here huh? Let's have a word with him." Jet smirked.

The three took off into the sky and caught up with them.

"Well well well, if it isn't Sonic the Hedgehog!" Jet said.

Sonic and Tails rolled their eyes knowing this wasn't a good time.

"Hey Jet, long time no see." Sonic said.

Jet noticed Sonic did not have his Extreme Gear.

"Where's your board?" Jet asked.

"Back in Station Square, me and Tails are here to set up a communications tower, and find the Wisps." Sonic explained.

"Lisps?" Storm was confused.

"No Wisps, with a W." Tails corrected him.

"What the heck are Wisps?" Jet asked.

"They are these aliens who are filled with this power called Hyper-go-ons that give any person they absorb amazing abilities." Tails explained.

Suddenly, a wicked grin grew across Jet's beak and Sonic's eyes widened.

"Oh no Jet, don't do what I think you're gonna do."

But Jet says nothing and the Rogues quickly fly away making Sonic face-palm.

"Darn, now we got even more trouble." Sonic sighed.

"We'll fix this Sonic, let's try to find as many as we can before they do." Tails said.

Back with Shade, she sighed happily when Gordon finally arrived at his designated station to let passengers off. Shade got off and quickly left the station, she had put back on her helmet and was now looking for a suitable area to rest. She found one of the windmills nearby and decided to rest there, unaware of the growing danger. A few minutes later she heard laughing and looked up. There were the Babylon Rogues who raced by and oblivious to her.

"Who were they?" Shade wondered.

Before she could think about anything else, Sonic and Tails could be seen above, Shade recognized them and hoped they would see her.

"Hey Sonic look, is that Shade?" Tails asked.

"Whoa it is. What is she doing here?" Sonic wondered.

They flew down avoiding the Windmill's blades and landed next to her.

"Shade! It's been awhile." Sonic said.

He and Shade shook hands as Shade took off her helmet.

"It's nice to see you again." Shade smiled.

"What are you doing here?" Tails asked.

"Traveling, though I did see some birds on boards go by."

"Oh no, the Rogues keep getting away. We're trying to find our friends the Wisps. Think you can help us find them?" Sonic asked.

"Sure, what do they look like?"

Sonic and Tails look at each other realizing they had a lot to explain.

"Well...let's just say if you see any small colorful and floating aliens, that's them." Tails said.

Shade nodded.

"Tails I say we split up to cover ground. I'll take Shade while you find Tidmouth Sheds and get that tower ready." Sonic said.

"You got it." Tails said.

After he left, Sonic and Shade raced down a line, Shade managing to keep up thanks to Sonic slowing down.

"So what can these aliens do?" Shade asked.

"Oh you'll see, I wouldn't be surprised if they were doing stuff to an engine as we speak." Sonic smirked.

With Thomas, he was just coming back to Tidmouth Sheds where James was the only one there.

"Hello James, anything exciting happen today?" Thomas asked.

"Not yet, I haven't been given a job today." James sighed.

As Thomas backed in, the cyan wisp came over after getting lost from the crash. He saw Thomas and James and had an idea. Most of Yacker's friends were very mischievous and known to play pranks. He floated in front of the engines surprising.

"Whoa, what are you?" Thomas asked.

The wisp spoke but the engines couldn't understand him.

"Um, what language was that?" James asked.

The wisp face-palmed from forgetting that no one outside their planet could understand them. Suddenly the pink wisp came crashing straight into the cyan one who shoved him away. Thomas and James watched in confusion as the wisps argued before suddenly coming to a decision. The cyan wisp raced straight towards Thomas and absorbed him.

"WHOA! WHAT!" Thomas gasped.

LAZER!

Thomas is suddenly transformed into a ball of energy that races straight into the distance like a lazer leaving James stunned.

"What just happened?" James asked.

Without a word, the pink wisp absorbed James.

"HEY, WHAT ARE YOU-"

SPIKES!

James turns into a spike ball and peels down the tracks chasing after the lazer-fied Thomas. Just as they leave, the Rogues arrive just as Yacker also arrives. Yacker had landed not too far from Tidmouth Sheds and was now looking for everyone. Before he could do anything, Jet snatches him up and they all land on the ground.

"Look here guys, one of those things from the ship." Jet held him up.

Yacker yelled and squirmed in Jet's grip but he wouldn't let go.

"Aw, he's so cute." Wave said.

"He's adorable." Storm chuckled.

"I wonder how much I'd get for him." Jet wondered.

Up until now, Jet had never explained his plan to the other two, and now that they knew...they were in disagreement with him.

"What? Jet you can't do that to this cute thing." Wave stomped a foot.

"For once I agree with her." Storm said.

Jet was shocked.

"WHAT? You actually care for these little creeps?" Jet asked.

"Jet we may be rogues and love to steal things, but I refuse to harm an innocent alien...no matter the cost." Wave snarled.

"Storm?" Jet tried to get his support.

"Sorry Jet." Storm shook his head.

Suddenly Wave shoved Jet hard enough to get him to let go of Yacker who hid behind her. Jet regained his balance and growled.

"Fine, I'm still gonna collect them, but you two go and find some treasure!" Jet ordered them.

Wave was about to yell at him but Jet had already taken off.

"JET YOU GET BACK HERE! RIGHT NOW!" Wave shouted.

Her sudden outburst caused Yacker to hide behind Storm instead. But Wave wasn't finished.

"HOW COULD HE TRY TO HARM THESE ALIENS! IT'S NOT RIGHT! IT'S NOT RIGHT I TELL YA! I MEAN SERIOUSLY, IF ONLY HE COULD-"

Storm and Yacker block out their hearing as Wave's rant is humorously sped up chipmunk style and she makes several hand gestures and awkward poses.

"This happens a lot." Storm whispered to Yacker who nodded.

Tails finally arrived stopping Wave's rant and he got out.

"There you two are, what happened to Jet?" Tails asked.

"Hey shorty, Jet went off to capture those aliens but he didn't tell us he was going to do that until just now. So we're not going to help him with that." Wave crossed her arms.

"Well that's good to hear. Think you can help us?" Tails asked.

"Sorry shorty, but we got other business to handle, one that doesn't involve harming the aliens." Wave said.

She and Storm got on their boards before Wave thought of something.

"Wait, why are you here?" Wave asked.

"Just setting up a communications tower, this place has been getting attacked lately and it's time we provide some assistance. Want to help?" Tails offered setting how his tools and a large box containing the parts for the tower.

Tails expected an insult or a scoff, but Wave was actually thinking.

 _"Hmm, this would be my chance to show shorty how much he could approve on his tech!"_ She thought.

Tails saw Wave's common evil grin and braced for the insult, but it never came.

"Sure shorty, hey Storm think you can look for treasure on your own for now?" Wave asked.

"Sure, this should be fun!" Storm nodded.

With him gone, Tails and Wave went to work while Yacker left to find his friends, little did he know...they were going to cause a lot of confusion and delay...

 _ **To be continued...**_


	6. Wisps PT 2

Chapter 6: Wisps PT 2

The Wisps, seeing that Yacker wasn't around to scold them, decided to play tricks on some of the engines, and avoid Jet at all cost. While color powers of Lazer and Spikes were in Thomas and James, Percy was about to experience the drill ability. Percy was pulling some more trucks and was getting ready to go up Gordon's Hill, but the trucks were pulling him back.

"HOLD BACK! HOLD BACK!" They chanted.

"No, not today trucks." Percy groaned.

But the trucks didn't listen and continued to pull back, suddenly a yellow wisp flew by and saw Percy was in trouble. Percy was amazed by the strange alien.

"Hello, what are you?" Percy asked.

The wisp knew Percy wouldn't understand so he simply absorbed Percy who gasped.

"Huh? How did he-"

DRILL!

Suddenly Percy and the trucks turn into a large drill and they dig straight through Gordon's hill and end up on the other side where Percy and the trucks turn back to normal. Before Percy could say thank you he was already racing down the hill fast but safe enough. The yellow wisp simply flew away satisfied, only to be found by an angry Yacker. Over at the quarry, the blue wisp found Edward loading up a few trucks with coal and flew over.

"Ugh, so many trucks, so much coal. But I must get the job done." Edward sighed.

The blue wisp suddenly absorbs Edward who gasps feeling the strange energy inside him.

CUBE!

Suddenly Edward turns into a large blue cube that alters the coal inside the trucks as well turning them into cubes. The effect also turned all the coal in the hopper into cubs when they came out. When all the trucks were filled, Edward reverted back and eventually the coal. The blue wisp quickly escaped before Edward could notice.

"What was that all about?" Edward wondered.

Henry had just finished delivering a goods train to one of the stations and Sir Topham Hatt stood on the platform pleased.

"Well done Henry, now you can go and rest." STH said.

"Phew thanks sir, my wheels are aching. Maybe I'll go over to that siding over there, Tidmouth Sheds is far away from here." Henry looked to his left.

The siding was 3 tracks over, but before Henry could move, the green wisp flew in front of Henry who gasped.

"What is that?" Henry gasped.

Sir Topham Hatt was confused as well. But as Henry tried to back up, the wisp absorbed him.

HOVER!

Henry turns into a spaceship-like form and floats over to the siding before turning back to normal, the wisp comes out laughing. Suddenly Yacker and the yellow wisp arrived and Yacker began to scold his friend.

"What were you thinking?" Yacker snarled.

"Sorry, it was just too much fun!" The green wisp said.

"Ugh, come on we need to find the others before that green hawk and get a hold of them." Yacker dragged him away.

Henry had no words for was he just witnessed or experienced and STH was at a lost. Back with Thomas and James they were actually having fun with the two wisps. They raced down the track laughing just as they turned back to normal.

"That was fun!" Thomas said.

"Yeah, so much speed. I bet we could challenge Gordon any day." James smirked.

Suddenly they hear Toby's bell from behind, he came up on a third track going faster than usual but he hadn't changed shape.

"Woah Toby, did you find one of these too?" Thomas asked.

"Yeah, it was a strange white alien that just absorbed me." Toby said.

The white wisp waved to the other two who waved back.

"Just like us...hey we should find Gordon so we can surprise him." Thomas said.

"That's a splendid idea." James agreed.

Just then they hear Gordon up ahead pulling the express.

"Perfect timing." Thomas smirked.

Meanwhile, Sonic and Shade were still racing around the island with no luck at finding any wisps.

"Man, those Wisps could be anywhere." Sonic sighed.

"Maybe that Yacker guy you were talking about has found a few." Shade thought.

"Probably, hey there's Storm." Sonic pointed out.

Storm spotted them and lowered down.

"Where's Jet?" Sonic asked.

"Uh he's trying to capture the Wisps. But me and Wave decided against that...I'm trying to protect the Wisps." Storm said.

"Where's Wave?" Sonic asked.

"Back at uh...that place where all the engines sleep." Storm forgot the name.

"Ah Tidmouth Sheds, I hope Tails finished that communications tower." Sonic said.

"You keep looking, we'll head over to the sheds to find them." Shade said.

Storm nodded and blasted off in a different direction. Back with Thomas, he, James and Toby were catching up with Gordon...but so was Jet.

"Aha! More of those aliens!" Jet smirked.

The three wisps dodged out of the way as Jet tried to grab him.

"Hey! Stop!" Thomas demanded.

"Or what? These guys are coming with me." Jet said.

They were distracted by Gordon blowing his whistle as they caught up.

"GORDON! I BET YOU'RE NOT AS FAST AS US THIS TIME!" Thomas called.

Gordon heard him and slowed down so he was tied with them.

"Oh please Thomas, I'm much more faster than you will ever be. We both know that." Gordon scoffed.

"Well not today Gordon, we got alien powers." James said.

"What? Alien powers? What silly nonsense is...WHAT?"

The wisps came into view after dodging another attack from Jet.

"What are those things?" Gordon asked.

"What we need to pass you that's for sure." Toby teased.

The Wisps quickly absorb the three much to the surprise of Gordon and Jet.

LAZER!

SPIKES!

With the white wisp not having a shout, Toby blasts off in the distance while James morphs into a Spike ball and Thomas morphs into a lazer and they blast off too leaving Jet and Gordon dumbfounded.

"Such amazing power! With those aliens I'll finally be faster than Sonic." Jet grinned.

As he shot past Gordon, the big engine felt embarrassed. At this point, Yacker with his friends complaining.

"Seriously, you've couldn't hurt him!" Yacker sneered.

"What? I was helping him!" The green wisp said.

"Well I'm sure you'll confused a lot of people as well." Yacker said.

"Jeez Yacker when did you turn into such a bossy alien?" The blue wisp said.

"I'm just trying to keep the peace around here, you've definitely have been causing a lot of confusion." Yacker said.

"Well when we round up everybody, can we at least explore this place together?" The green wisp asked.

"Sure, hey have you guys seen crazy mouth?" Yacker asked.

"Nope. Why?" They both asked.

"Damn it." Yacker face-palmed.

Suddenly Sonic and Shade race over.

"YACKER! Long time no see!" Sonic said.

Sonic and Yacker high-fived. Yacker tried to explain to Sonic what's wrong but Sonic couldn't understand him without Tails' translator.

"Uh...I'm going to assume you're looking for your friends." Sonic shrugged.

Yacker nodded.

"Well come on, we need to check on Tails' communications tower, should be up by now. Oh and this is my friend Shade."

Yacker and the Wisps waved to her and Shade waved back, though a bit surprised. She was actually fascinated by their looks. They eventually arrive at the still empty Tidmouth Sheds where Tails and Wave were laughing.

"No way, Jet really tripped down the hall like that?"

"Yeah, he can be very clumsy sometimes!"

"Hey guys what's so funny?" Sonic asked coming over.

"Oh, Wave was just telling about this one time Jet was walking about of the shower up in the zeppelin and slipped down the hallway crashing into a wall." Tails said.

"You'd have to be there." Wave laughed.

"Oh man I'd pay to see that!" Sonic chuckled.

The Wisps floated around the large communications tower with awe. It stood in front of the sheds and was almost as high as it. It was very skinny and looked almost like the elevator used to get up to Eggman's intergalactic amusement park.

"With this tower, we'll be able to detect any danger that threatens this island. Every few minutes it will scan for any threat and will alert G.U.N., what do you think Sonic?" Tails asked.

"It's perfect, now the island will be safe, for now." Sonic shrugged.

The Wisps cheered together.

"Hmm, we still have a few more Wisps to collect. But where could they be?" Shade wondered.

"I wonder if Jet caught any." Wave worried.

"Nah, they're too smart for him. Heck I bet Storm will have a better chance." Sonic chuckled.

Shade however was rather unimpressed by Jet's loyalty to his team.

"Hmph, figures someone like him would mess up like this. He's probably making the whole island panic." Shade accused.

This seem to strike a nerve in Wave, true, Jet's current actions were wrong, but being self-centered and a bit mean was part of his personality.

"Hey, Jet can do some really stupid stuff, but he's not much of a threat to the island." Wave sneered.

"How old is Jet?" Shade asked.

"14."

"And how old are you and Storm?"

"I'm 18 and he's 19...why?"

"Figures, you listen to a little kid who'll act however he wants and you killed." Shade said.

Sonic, Tails and the Wisps sensed trouble. Sonic tried to defuse the situation.

"Uh, could we get back to the-"

"WHO DO YOU THINK YOU ARE?" Wave shoved Sonic back and growled at Shade.

"DON'T PUSH ME BIRDIE!" Shade growled back.

"OR WHAT?"

The two were literally in each other's face ready for one of them to take a swing, but Sonic this time managed to push them apart.

"Ladies we don't have time for this, we need to find those last remaining Wisps before Jet." Sonic said.

"Hmph!" The girls turned away from each other.

Tails sweatdropped and the Wisps hid behind him. Just then Percy arrived to see them all.

"Oh what's going on here?" Percy asked.

"Percy! Glad to see you, have you seen any more Wisps?" Sonic asked.

"Besides that yellow one there no. Is that what they're called?" Percy asked.

"Yep, they're from another planet." Tails said.

"Cool, hmm, maybe Thomas has seen some." Percy thought.

Just then the blue wisp arrived and cowered under Yacker's angry gaze.

"Sorry Yacker." He whimpered.

"Look let's just focus on finding the others." Yacker sighed.

Suddenly the tower picked up a signal and Tails grabbed his translator which now included the tracking system for the tower.

"I picked up some strange energy over by the main line, where Gordon pulls the express." Tails said.

"Then that's where the others are, LET'S GO!" Sonic said.

"Can I come?" Percy asked.

"Of course, lead the way to the main line." Sonic said.

And so while Wave got on her board, Sonic, Tails, Shade, and the Wisps aboard Percy except for Yacker who absorbed Percy and gave him a boost of speed as they raced towards the main line. With Storm, he was chasing after the purple and orange wisps.

"Come on aliens, there's no time for games." Storm groaned getting tired.

The two wisps had a devious idea, slowing down, the orange wisp flew straight at him and absorbed him before Storm could grab him.

"Oh no!" Storm gulped.

ROCKET!

Storm and his board suddenly transformed into a rocket and flew straight up into the air, and when he was high enough, the wisp left his body and Storm fell down trying to get on his board. But the purple wisp then absorbed him.

FRENZY!

Storm turned into into a creepy chomper-like creature and started to hop down the track and chomp through several empty buildings, bushes and walls. The orange wisp followed them laughing. But soon Percy and the group caught up and Yacker moved out of Percy making slow down.

"YOU TWO! KNOCK IT OFF!" Yacker yelled.

His next words surprised Tails and he showed the translator to Sonic and Shade who cringed. As the purple Wisp moved out of Storm, Wave went to check up on him.

"You okay Storm?" Wave asked.

"I've been better." Storm rubbed his head.

"They should be nearby, we need to hurry." Tails said.

And with the two wisps found, the group went to find the last three. When Percy arrived at a signal box, they all saw Thomas, James and Toby racing by with Jet and Gordon behind them.

"There they are!" Sonic said.

With Yacker's help, Percy raced past Jet and Gordon who were once again shocked.

"Now he has that power?" Jet asked.

Sonic leaped out and Jet saw him.

"There you are Sonic, took you long enough." Jet said moving alongside him.

"Jet, you need to stop this. These aliens are not yours to sell." Sonic sneered.

"We'll see about that won't we?" Jet moved forward. The other wisps stayed hidden in Percy's cab as Jet flew inside.

"ALRIGHT ALIENS, YOU'RE COMING WITH ME!" Jet snarled.

But he was met with a punch in the beak from Shade.

"You'll have to get through me first." Shade put up her fists.

"Alright usually I would never hit a girl, but this time I may make an exception." Jet put up his own fists and got off his board.

The Wisps backed away and Tails flew out to meet Sonic.

"What's going on in there?" Sonic asked.

"Oh just Shade and Jet about to fist-fight." Tails shrugged.

"Heh, I wonder what would happen if one of the Wisps absorbed Percy while everyone was inside." Sonic chuckled.

"That would be something, but what should we do?" Tails asked.

"I'd say let Jet have what's coming to him." Storm said.

"I agree it would serve him right." Wave said.

All the engines kept racing as Jet and Shade fought in Percy's cab. Jet was missing each of his punches but Shade managed to sock him in the chest and face a few times. Jet tries to swipe her off her feet but she jumps and kicks him out the cab with his board. Jet flips her off and flies in front of everyone.

"YOU'LL NEVER GET AWAY WITH THIS!" Jet snarled.

"JET IT DOESN'T HAVE TO BE THIS WAY!" Wave yelled.

"BOSS LEAVE THEM ALONE!" Storm yelled.

"QUIET! NONE OF YOU WILL CATCH ME! ESPECIALLY YOU SONIC THE HEDGEHOG!" Jet pointed at him.

Sonic leaped on top of Thomas and stared him down with a smile which confused Jet.

"I don't have to catch you this time." Sonic said.

"What do you mean?" Jet asked.

"Wisps, you know what to do!" Sonic said.

UNLIMITED COLORS!

All the Wisps nodded and flew in front of Sonic one-by-one and formed a circle.

LAZER!

DRILL!

SPIKES!

ROCKET!

CUBE!

HOVER!

FRENZY!

FINAL COLOR BLASTER!

Sonic leaped into the middle of the circle and together they rammed into Jet knocking him down towards the track and landed between them far in the distance. The engines and the Rogues could not believe such power was used. Gordon of course had to be redirected to another track and left the group to deliver his passengers. The others screeched to a stop in front of the defeated Jet.

"Ugh...blasted aliens." Jet slammed a fist on the ground.

"Sorry Jet, it was for your own good." Wave smirked.

"Yeah boss, you went too far this time." Storm said.

Jet hated the feeling of losing, but the embarrassment was even more upsetting. Yacker and the Wisps all cheered for Sonic while Tails and Shade clapped.

"Well done Sonic!" Tails said.

"That was amazing." Shade said.

"Aw thanks, we couldn't have gotten the job done without you guys." Sonic said.

Wave and Storm picked up Jet who grabbed his board. Sonic walked over to them.

"So Jet, if you ever feel like doing some actual racing instead of terrorizing aliens, come find me around Station Square, not here." Sonic wagged his finger.

"Hmph, whatever! You just got lucky this time." Jet sneered.

Storm laughed as Wave grabbed Jet by the large feathers on his head and yanked him away while he whined in pain.

"Come on Jet, we're leaving! Oh and see ya later shorty." Wave winked at Tails.

"Yep, same old Wave." Tails sighed.

"Shorty?" Shade giggled.

"Don't say that please." Tails groaned.

But it was too late when Shade and Sonic burst into laughter. Of course the Wisps and engines didn't get it. Later that night with all the engines in the shed and Toby next to them, Tails explained to Sir Topham Hatt about the tower and he thought it was an excellent idea.

"Well done Tails, this will be very useful." STH nodded.

"Glad you like it sir, now all I have to do is fix Yacker's ship." Tails rubbed his forehead.

"So I guess this means we're staying for awhile, what about you Shade?" Sonic asked.

"I don't plan to leave this island yet...there's so much to do." Shade smiled.

"That's what I'm talking about!" Sonic gave her a thumbs up.

Meanwhile, Thomas, James and Toby were looking at Gordon.

"So Gordon, were you impressed?" Thomas asked.

"What? By everything that happened, of course! But you only went faster because of those Lisps."

"Wisps!" Everyone corrected him.

"Oh sorry, but that's the only way. I'm still the fastest engine around...at least when Spencer isn't here." Gordon muttered.

"The wisps are wonderful aliens, I bet they'd make any job easier." James said.

"Maybe we'll find out soon." Toby said.

"As long as they give us a warning next time." Henry gulped.

"Uh Yacker...where did the Frenzy one go?" Tails asked.

Everyone looked around but didn't see him, suddenly Henry felt something strange.

FRENZY!

"Oh no, not again!" Henry groaned.

Everyone gasped when Henry turns into the chomper-like creature and goes hopping away down the track away from the sheds.

"Uh-oh, here we go again!" Sonic smirked.

Yacker face-palmed as he and Sonic went to catch the crazy Wisp knowing Henry was not going to be sleeping well tonight!

 ** _END OF ARC 3._**

 ** _To be continued in ARC 4: METAREX MAYHEM!_**


	7. Metarex PT 1

_**While the Metarex are from Sonic X, for this story they will exist in the game universe and Sonic and his friends know them. Here the Metarex are still evil but not to be taken seriously since they will most likely be out of character for humor reasons.**_

* * *

ARC 4: Metarex Mayhem

Chapter 7: Metarex PT 1

A week has passed since the Wisps landed on the Island of Sodor and Jet the Hawk was defeated. The communications tower continued to scan the Island every few minutes and everything was safe. How much more chaos could the island handle? Well the chaos wasn't over yet, for a new force was about to make it's way over and disrupt the peace yet again.

After fixing up Yacker's ship, Sonic, Tails and Shade had stayed for awhile and were touring the island with the Wisps. Yacker and the Wisps had planned to stay just a little while longer before heading back to their planet. One day, the engines gathered at Tidmouth Sheds where Sir Topham Hatt needed to talk to them.

"Okay everyone, I know we've had a rough month so far, robots rampaging, evil knights invading and even come cute little aliens came to play. But, we all know that we must keep the island safe at all costs." Sir Topham Hatt said.

"Sir, do you think this is all leading up to something big?" Thomas asked.

"I don't think so Thomas, besides those knights, we never really had a real threat to the Island." Sir Topham Hatt shook his head.

"Hmm." Thomas went into thought.

"Anyways, we have nothing going on now. So I expect to all to get some jobs done today." STH said.

"Yes sir!" They all whistled.

And so after STH gave out the jobs, only Thomas, Percy and Edward were left in the shed. Percy noticed Thomas seemed to be on edge.

"What's wrong Thomas?" Percy asked.

"I just feel like something bad is going to happen." Thomas sighed.

"Like what?" Percy asked.

"Well, maybe something from...up there." Thomas looked to the sky.

"You mean space? Why would that happen? Even if there was something coming from space, they wouldn't come here!" Edward said.

"I'm not too sure, Metal Sonic flew here, that evil King Arthur invaded here, and now we have those Wisps that crashed here. I don't think I'll be surprised if something else happens again soon." Thomas said.

"But as long as we have this tower, G.U.N. will come to the rescue, in fact Sonic did say that some G.U.N. troops would be placed here." Percy said.

"True...ugh...I just need to go clear my head. I'm gonna go shunt." Thomas left.

Percy and Edward felt sorry for Thomas, but he had been through so much...and his problems were nowhere near close to done.

 ** _Far up in space..._**

The Metarex mothership was busy flying through the Galaxy in hopes of finding all the planet eggs and destroy all animal life. But while that was their main goal...they were taking a little break. The plant robots obviously known as the Metarex were busy walking around the ship talking and trying to find something to do. Many had gathered in a large room where a little party was being held. Currently everyone was watching as Black Narcissus and his gold and silver troopers were dancing to a song in the middle.

"Hah! They all love my style. I am the best dancer on this ship." Narcissus said.

When the song finished, everyone cheered them on. Nearby, Pale Bayleaf was playing chess with the Metarex Kingape. Said monkey-like robot was losing.

"Ugh, how do you get so good at this?" He asked.

"Simple, unlike the others, I'm a profession at skill and concentration. And this is nothing but child's play. But I do admit that you're the first to last this long, maybe your skills are almost up to par with mine." Bayleaf said.

"Really?"

"No."

"Aw."

"Checkmate."

"DARN!"

"Someone's having a bad day." Narcissus came over.

"Not really, did you have fun embarrassing yourself?" Bayleaf teased.

"Embarrassing myself, hah, everyone loved me over there."

"I'm sure."

Then the monkey metarex growled when the gold and silver troopers laughed at him for losing.

"DOH! WHY YOU LITTLE ASSHOLES!"

He chased the two out of the room and down the hall.

"Those three are so immature compared to the rest of us." Narcissus sighed.

Bayleaf got up to leave.

"And you aren't?" Bayleaf teased.

"I'm more mature than Dark Oak himself."

"Keep telling yourself that."

Meanwhile, the leader Dark Oak was in the control room sitting in a chair and looking out at space. He seemed to be in deep thought as he clicked his long metal claws together. He had only ordered the break as they had conquered many planets in the past, but the crew had grown tired and surprisingly their group had lost many. A console sat on front of him and he began to scan other planets nearby out of boredom. Eventually he set his scanners upon Mobius...but currently he wasn't interested in the Planet Egg since he could get it some other time...as long as that pesky hedgehog didn't stop him.

"Hmm, what is this I'm detecting, some kind of strange...but strong energy." Dark Oak looked closer.

He zoomed in on the planet and the saw some strong energy coming from the Island of Sodor, it wasn't the Planet Egg energy either, that was much weaker. Dark Oak pulled up some information on the island to find out what was on it. No info listed the Wisps, only the engines themselves.

"Hmm, sentient machine-like robots...intriguing." Dark Oak said.

Just then he could hear arguing outside the room and when the door opened, Red Pine and Yellow Zelkova walked in having a heated conversation.

"You couldn't rule even a small island with that thick head of yours!" Red Pine snarled.

"I'm just as smart as you four and I could rule anywhere if I wanted to. And also you need to quit complaining about this break." Zelkova sneered.

"That's why I'm here to talk to Dark Oak, we should be continuing to invade these planets for their planet eggs, not partying!" Red Pine argued.

"Well I like to party!"

"You and all the other idiots."

"WHAT DID YOU SAY!"

"YOU HEARD ME!"

"WHY YOU LITTLE-"

Dark Oak decided to tune them out just in time as the two lunged at each other starting up a cartoon dustcloud fight. He continued to do some more research just as Black Narcissus and Pale Bayleaf came in seeing the fight and Dark Oak ignoring them.

"Ugh, this is like the 5th time this month they've fought." Bayleaf face-palmed.

"I find it quite entertaining, the troopers fight all the time as well." Narcissus chuckled.

"Well I bet you'd like to join them."

"Pfft, as if! I'm not getting my armor scratched up." Narcissus scoffed.

Unfortunately, he was standing too close and got punched accidently by Red Pine's clawed fist.

"OW! OH HELL NO!"

Bayleaf face-palmed a second time when Narcissus jumped right in. Bayleaf then walked over to Dark Oak to see what he was doing.

"Sir, what is all this?" Bayleaf asked looking at all the popped up screens.

"I found an Island on Mobius that has some strange energy coming from it. But not only that, look here, the Island also seemed to be full of sentient machines...trains are what they're called." Dark Oak pointed out.

Bayleaf examined the information with great interest.

"Hmm, I bet if we were to take over and grab one of them, we can add a new powerful ally to the Metarex, with some heavy modifications of course. The question is...which one is truly worthy?" Bayleaf crossed his arms in thought.

"The only way we'll find out is to go down there and take over...as long as that pesky hedgehog won't be around." Dark Oak clenched his claws into fists.

"I doubt he will, besides, he'll have to get through all of us to take the island back. Surely we're sending in some troopers as well right?"

"Of course, now then...we just need to stop those 3 idiots."

Dark Oak turned around and yelled.

"WOULD YOU 3 KNOCK IT OFF ALREADY DAMN IT!"

Dark Oak's voice boomed throughout the whole mothership and the 3 stop immediately and the cloud vanishes.

"Sorry sir." They whimpered.

"Now then, gather some of the troops, we're planning an invasion on that island!" Dark Oak popped the map of the island on some bigger monitors.

"An Island? Why just that? Aren't we going to get the planet egg as well?" Red Pine asked.

"In time, but we're going to gather some new allies. This island is infested with sentient machines that could prove useful. We're going to find some and reprogram them to my specifications. Sonic will have no idea what hit him!" Dark Oak evilly laughed.

"Hah, I bet I'll find the best one!" Zelkova yelled.

"Sure you will, I'll figure out the best one." Red Pine scoffed.

"ENOUGH! GET DOWN THERE NOW!" Dark Oak commanded.

And so after gathering at least 50 troopers, including the gold and silver one, the Metarex leaders all headed down towards the Island in their own personal battleships while some of the remaining troopers kept the Mothership in space where their party continued.

 _ **Sodor...**_

Thomas had finished shunting some of the trucks and was taking a break next to the shed with Annie and Clarabel.

"I say Thomas, you look paranoid." Annie said.

"I am, I'm just worried about the next attack to this island." Thomas sighed.

"Oh please Thomas, anyone else who dares invade this island has to be a fool." Clarabel said.

"I guess you're right, as long as we have that tower up, we should be fine." Thomas smiled.

"That's the spirit Thomas." Annie chuckled.

But Thomas wasn't the only one on the lookout. Besides Sonic, Tails, Shade and the Wisps, any of the engines across the island kept watch for anything wrong, some people began to fear but were sure that if anything happened, the great Sonic the Hedgehog would take care of the problem. Awhile later, Thomas was out for a little run around his branch line alone when he saw a strange shadow cover him.

"Huh? What is that?" Thomas asked.

One of the Metarex battleships flew by past him and Thomas knew the danger was back.

"Not again, I knew it. I got to get to the tower!" Thomas decided.

From in the ship which was Dark Oak's, he examined the little engine.

"Hmm, this one seems like a nice fit. Plus the energy readings are getting stronger." Dark Oak said.

The energy which was coming from the Wisps wasn't anywhere near Tidmouth Sheds, but Dark Oak planned to find it at some point. Apparently Thomas was leading him to some tower.

"Whatever this tower is, I'll find it and destroy it." Dark Oak said.

Then above him, the other 4 appeared on large screens.

"Any progress sir?" Bayleaf asked.

"I've made contact with one of them and I'm chasing him now to some tower he mentioned. You 4 take over any large locations you can find, then we will find our suitable captive." Dark Oak commanded.

"Yes sir." They all said.

Thomas raced faster and faster and managed to past the lowering ship. Some other engines began to notice the other battleships arriving and zooming around the island. Some people began to panic and run for cover and the some of the engines had to hide. Tails was flying his plane with Sonic and Shade on the wings and they noticed the ships as well.

"Those look familiar." Sonic said.

"You don't think it's..." Tails trailed off.

"Only one way to find out." Sonic said.

"Here we go again." Shade sighed.

Meanwhile, Yellow Zelkova noticed Harold the Helicopter up ahead.

"Ooh, maybe I could blast him down!" Zelkova said.

"Not yet, we're trying to claim the island not destroy anyone." Bayleaf said over their links.

"Ugh, fine!" Zelkova pouted.

Luckily Harold saw the ship getting closer and veered out of the way nearly running to Jeremy the jet who also lowered down to escape the battleship's rampage. Red Pine studied the Island map to figure out the best place to land...possibly the Smelters Yard.

"Hmm, maybe I could find something useful around here." Red Pine thought.

Pale Bayleaf flew over the Narrow Gauge Railway and saw how small these engines were...maybe he could use that as an advantage. And at the same time he'd find the source of the energy. Black Narcissus found the quarry and looked at with disgust.

"Ugh, I'll definitely get dirty around here." He scoffed.

Dark Oak contacted him.

"Doesn't matter Black Narcissus, land there immediately!" Dark Oak snapped.

"Fine sir." He groaned.

Dark Oak continued to chase Thomas towards Tidmouth Sheds which was getting close, but Dark Oak wouldn't let him win.

"This mech has determination and is pretty fast for being one of the little ones." Dark Oak said.

As they arrived at the empty Tidmouth Sheds, Dark Oak blasted ahead and landed right in front of the sheds. The communications tower had just did another scan of the island and detected the Metarex as a threat. But just as it started to send info to G.U.N., Dark Oak blasted the top half of the tower, while it remained standing, it was heavily damaged and only a bit of the info managed to be sent. Thomas screeched to a halt and got on the turntable just as Dark Oak exited. Dark Oak didn't expect to be only a few inches taller than Thomas.

"Who are you?" Thomas asked fearfully.

"I am Dark Oak, leader of the great and powerful Metarex. We have come to take over this little Island and capture one of you to be part of our Metarex army, so that we may conquer this planet and steal the Planet Egg. We plan to wipe out all animal forms on this planet so PLANTS WILL RULE!" Dark Oak shouted.

Thomas gasped, this was terrible...much more dangerous than King Arthur's takeover or Jet trying to steal the Wisps.

"Uh...who exactly would you be looking for? I couldn't be chosen for such a thing." Thomas said.

"Oh I beg to differ, I studied you and some of the others. And I've looked at the past reports, a robot doppelganger of Sonic taking refuge on this island, some knights from another reality failing to conquer this island, and some strange aliens with different powers visiting. Now that I think about it, I bet those aliens are the cause of the strange energy I detected from space. And after all those problems, there seems to be only one being that always gets caught up in the middle...YOU!" Dark Oak finished pointing a long metallic claw at Thomas.

Thomas had to admit that he was right...he was involved the most in everything so far...and now he was going to be involved with the Metarex.

"I don't know what makes you so special, you're little. Then again, your fast, determined and brave...something I can really use in the Metarex to give us an even greater advantage. But...while the others are looking for more of your friends to check out...I think I'll issue you a little challenge." Oak sneered.

Thomas gulped, he'd rather have Omega challenge him again. This robot looked very intimidating and he knew to take him seriously.

"What kind of challenge?" Thomas asked.

"I'd like to see how long it will take for you to evade my attacks and flee, since apparently you're stuck to these rails and can't fight, I'll go easy on you...for a bit." Dark Oak said.

Then the few number of troopers he brought in his ship came out.

"Metarex, secure this area, let no machine near it. I'm going to be busy." Dark Oak glared back at Thomas.

"Oh boy." Thomas groaned.

Thomas spun back around on the turntable while Dark Oak floated up beside him.

"Let's see if you got what it takes to get away from me! I'll give you a 10 second head start." Dark Oak said.

Thomas said nothing and chuffed away quickly, he had to get away from this guy fast, and hopefully not run into any more of them...of course that wouldn't be the case. Dark Oak received contact from the other commanders that they have found certain locations to mark their territory and Dark Oak scanned the island for the locations, he needed to lure Thomas to each one.

"Metarex, I have located a suitable candidate. Make sure you give him a hard time when he arrives." Dark Oak said.

He sent them the info on Thomas and they answered back.

"A little train? Surely you're joking. This will be easy!" Red Pine said.

"Interesting, he just may work." Pale Bayleaf said.

"Hah, I'll let him know just who he's dealing with." Black Narcissus scoffed.

"I'LL SMASH THAT TRAIN TO PIECES!" Yellow Zelkova yelled.

"NO!" The other four yelled at Zelkova who cowered.

Dark Oak then ended the contact and chased after Thomas...unknown to him...Yacker had just arrived a the sheds worried. He saw the damaged tower and hoped the signal got through. Thankfully for him, Sonic, Tails and Shade were arriving as well.

 _ **G.U.N. HQ...**_

Shadow and Rouge were trying to track what they could of the signal...but it weak.

"It's back on that island I think. Maybe this would be a good chance to find more jewels." Rouge smirked.

"Hmph, I'd expect that from you. Too bad the signal is weak, we can't even tell what the threat is or if we even need to bring some troops." Shadow said.

"I'm sure Big Blue and Fox Boy are already looking for the threat." Rouge said.

"I bet they couldn't handle it by themselves, not even those engines could take care of themselves."

"Don't underestimate them Shadow, you never know, one day they'll surprise you."

"..."

"I'm guessing the silence means I'm right. Anyways I'll get Omega, knowing him, he'd want to race that blue engine again." Rouge walked away chuckling.

Shadow just stared the map of the island on the screen. What if she was right?

 _ **To be continued...**_


	8. Metarex PT 2

Chapter 8: Metarex PT 2

Thomas raced as fast as he could across the island with the evil Dark Oak catching up quickly. The Metarex leader laughed evilly.

"I have a few surprises for you Thomas! And you're gonna love them!" Dark Oak sneered.

"Not looking forward to them." Thomas shouted.

Dark Oak flexed his long metallic claws and scratched Thomas on the right side ruining the number 1.

"OW!" Thomas yelped.

"Oh there's more where that came from." Dark Oak said.

Dark Oak flew onto the other side, clenched a tight fist and punched Thomas' left side making a dent.

"OW! STOP THAT!" Thomas yelled.

"LET'S SEE YOU GET PAST THIS!" Dark Oak said.

He brought out his long sword, flew ahead and sliced the tracks in front of him, but Dark Oak hadn't taken account that he had sliced the tracks that were ahead of the points. Thomas instead moves onto another line missing the broken track completely. Dark Oak never bothered with the signal box and kept going.

"Lucky shot, but I won't miss again." Dark Oak said.

He moved ahead to slice the track again, this time Thomas had no way to avoid it. But the force of the slice caused both ends of the track to bend upwards. Thomas shut his eyes as he flew up, catching some air from his speed, and Dark Oak has no time to react when Thomas collides with him sending the Metarex leader flying behind him and Dark Oak digs his claws into the roof of Thomas' cab to stop himself. Thomas lands on the track perfectly and Dark Oak slips inside the cab. Out of anger he punched out the glass windows.

"I would disable you from here, but that would be the easy way out." Dark Oak said flying back out.

From there the two raced past a few surprised engines and people. From above Sonic, Tails and Shade looked out for any Metarex, but unfortunately they had just missed Thomas and Dark Oak. Over by the Dieselworks, Yellow Zelkova had claimed the building but the Diesels were complaining.

"There's no way we'll let you stay here!" Diesel said.

"Ooh I'm so scared, you guys are stuck on those rails. What could you possibly do?" Zelkova said.

He walked onto the little elevator-like platform and raised up to the top level where all the Diesels were. His little team of Metarex troopers were back on the bottom level laughing and chatting. Diesel, Arry, Bert, Den and Dart knew nothing could be done, and they never wanted to be involved.

"Look, we got nothing you want." Arry said.

"Exactly." Bert said.

"I know you don't, but Dark Oak said that I should claim anywhere I want, and find a suitable engine to turn into an ally. And none of you are worthy, none of you are strong as me, as tough as me, AS POWERFUL AS ME! HAHAHAHAHAHA!" Zelkova laughed.

With his back turned towards the diesels, the leader of the diesels...Diesel 10, emerged quietly from his part of the building. As he got closer, he knocked Zelkova in the back with his claw.

"HUH? WHO DARES-"

He doesn't finish when Diesel 10 grabs him in his claw and throws him down below. All the diesels begin to laugh at him.

"ARGH! WHY YOU..."

Zelkova clenched his fists tightly and lunged straight up at him. Diesel 10 tried to grab him again, but Zelkova leaped on top of the claw and landed on the roof.

"GET OFF ME!" Diesel 10 yelled.

But then Zelkova ripped the entire claw off the roof, jumped down and slammed the claw into the back of Diesel 10 knocking him off the platform and landing on the bottom causing some of the troopers to jump away in time. Diesel 10 had not landed on the track correctly.

"Uh-oh..." Diesel 10 gulped.

Zelkova jumped down and growled.

"YOU THINK YOU CAN STOP ME? PATHETIC!" Zelkova scoffed.

Before Diesel 10 could say anything, Zelkova charged him and rammed him hard onto his side.

"TAKE THAT! HA-HA! I'M UNSTOPPABLE!" Zelkova yelled.

"Ugh..." Diesel 10 groaned.

"ALRIGHT WHO'S NEXT?" Zelkova turned to the others.

The diesels all back away in fear.

"Thought so."

Just then he receives a contact.

"Zelkova be ready, I've got Thomas on the way." Dark Oak said.

"Got it sir."

Zelkova raced out of the Dieselworks while some troopers followed to watch. As Zelkova reached the line that passed the Dieselworks, he saw Thomas and Dark Oak up ahead. Thomas gasped seeing the much bigger Metarex commander up ahead.

"Oh this should be fun!" Zelkova cracked his knuckles.

Thomas figured stopping wouldn't be such a good idea, and so he continued to charge him.

"Ooh, he wants this to be a test of strength eh, well that's easy for me."

Zelkova charged Thomas like a raging bull and Thomas charged back.

"YOU WON'T GET PAST ME!" Zelkova snarled.

The two collide and enter a power struggle. Thomas continued to spin his wheels while Zelkova held onto him, digging his fingers into Thomas' sides. He was a bit bigger than Thomas but was surprised by how much strength Thomas had. He stared him down.

"You're strong I'll give you that, but not even you are worthy of becoming one of us."

"I never wanted to be!" Thomas said.

"That's good, besides, you're nothing but a little blue wimp!" Zelkova snarled.

Dark Oak watched nearby, maybe Thomas had the ability to join after all, and Zelkova was just underestimating him. The two continued to push back and forth, Thomas' wheels slowing down and struggling to go forward.

"I'LL THROW YOU OFF THE TRACK!" Zelkova snarled.

But before he could try, Thomas stops pushing all together and backs up confusing Zelkova who let go.

"Huh? What are you doing?"

"Oh just moving onto another line, there's a another engine coming." Thomas said.

Dark Oak expected Zelkova to fall for it, and he did.

"Huh where?" Zelkova turned around.

Thomas took his chance to charge Zelkova again and this time rammed him down and knocked him onto another track.

"Idiot." Dark Oak snarled.

Dark Oak continued his race with Thomas while Zelkova ended up getting laughed at by his troops.

"SHUT UP!" Zelkova yelled.

Suddenly he is sucker-punched to the ground, getting up quickly he sees E-123 Omega standing there.

"Pathetic threat to Island will be defeated." Omega snarled.

"Ah, a worthy opponent, BRING IT!"

And the two lunged at each other. Meanwhile, Shadow and Rouge had arrived and were defeating the troopers left at Tidmouth Sheds and were winning easily. Most of the Metarex weren't at their full strength at the time. When the sheds were saved, Shadow looked over at the tower.

"Looks like the tower was damaged." Shadow examined it.

"Then I guess Fox boy will have to fix it again, I guess we should go look for more." Rouge thought.

Just then Sir Topham Hatt arrived in his car.

"Goodness me, what happened here?" STH asked.

"The Metarex have been dealt with, I'm assuming the engines are hiding?" Shadow asked.

"Hopefully, I hope Sonic is helping out." STH worried.

"I'm sure big blue is, and maybe some of the engines as well." Rouge said.

Shadow only turned around crossing his arms and closing his eyes. He was still in doubt about how any of the engines could help. His thought is interrupted when they see Sonic and co. lowering down towards them.

"Hey guys, glad to see you here. Huh, I guess the Metarex were easy to beat." Sonic said.

"They were too weak." Shadow said.

"I hope Omega is behaving himself...then again...it's Omega." Rouge sighed.

Shade came down and shook hands with Rouge.

"Nice to see you again." Shade said.

"Likewise, I assume you're traveling?"

"Yes, though this was not what I expected to be faced with." Shade chuckled.

"Hey Sonic, we need to find Yacker before the Metarex find them." Tails said.

"Right you three head on up in the air, me and Shadow will cover from here." Sonic said.

"Together?" Shadow glared at him.

"Shadow this is not the time for arguing, we got a job to do." Sonic said.

Sonic raced off and Shadow followed a second later. Tails looked at the damaged tower.

"Oh no the tower, I got to fix it when we're finished here." Tails said.

Shade jumped back into the plane while Rouge took to the air. Back with Red Pine, he was searching around the Smelter's Yard for something useful, he shoved away some old engine parts and a few lone trucks.

"They could at least organize around here...ugh." Red Pine said.

His few troopers searched different piles finding a few engine parts like funnels, wheels and buffers but nothing of interest.

"Hmm, there has to be something."

Suddenly Red Pine nearly trips into the melting pit down below at the edge of the building. Curious, he grabbed an old wheel and tossed it in, it melting immediately as it sunk.

"Hate to be that unlucky person." Red Pine backed away.

Dark Oak continued to try and attack Thomas but the engine kept slowing down or speeding up to dodge his sword. As Dark Oak prepared to strike Thomas' boilder, he is bombarded by the Wisps who surround him.

"AUGH! GET AWAY FROM ME!" Dark Oak swatted them away.

He punched, kicked and clawed at them but kept missing. Yacker moved ahead to see Thomas. He motioned for Thomas to hide over at the Smelter's Yard while they dealt with Dark Oak. Thomas whistled and quickly left onto another track and thankfully Dark Oak was distracted. Thomas raced inside the Smelter's unaware of the threat inside. He stopped and looked around...he could see no one else in the red mist. Some machines nearby hummed and some hanging chains knocked against each other.

"I hope everyone is alright." Thomas sighed.

"I wouldn't think so." Came a voice.

"Huh? Who's there?" Thomas asked.

Suddenly, Red Pine emerged from behind him and trailed his sharp claws lightly against Thomas' side with the dent.

"Number 1 huh? They'd really give you that number, you're pretty small to be number 1 around here." Red Pine teased.

He came in front of Thomas and the troopers came out of hiding.

"How many of you guys are their?" Thomas asked.

"Four commanders, one leader, but countless troopers...scared?" Red Pine asked.

"Not as much as I should be, I already took down that yellow one."

"Hah, Zelkova is an idiot. Even with brute strength he couldn't even beat a little runt like you. I assume you're the one Dark Oak is choosing...poor choice if you ask me."

"Well I'm not going with any of you." Thomas said sternly.

"Oh really? You can't stop us all! Especially me!"

Thomas moved forward trying to ram him but Red Pine jumped out of the way.

"Nice try, but it will take more than that to defeat me."

While the Wisps distracted Dark Oak, Yacker flew in and saw Thomas needed help. Thomas' next tactic was to let off steam, the steam mixed with the red steam of the Smelter's Yard and covered everyone.

"EUGH! I CAN'T SEE!" Red Pine yelled.

Thomas moved forward heading for the exit, but Red Pine heard him.

"NO! STOP HIM! CLOSE THE DOORS!" Red Pine ordered.

Yacker managed to get away from the smoke and started to throw large objects at the troopers like large wheels, pipes and tripped them with chains. The Metarex that were not damaged began to argue with each other over the failing mission and eventually a brawl erupted between them. Yacker fiddled with the controls to the large crane and put Red Pine as the target. As the smoke was clearing, Red Pine was trying to pull Thomas towards the melting pit.

"YOU'RE FINISHED!" Red Pine yelled.

"NO!" Thomas yelled.

Yacker pressed a red button that caused the crane to come down on Red Pine and grab him.

"Huh? What the? LET ME GO!" Red Pine struggled.

The crane lifted him up and he stayed there, giving Thomas time to escape, ramming through the fighting troopers and out of the Smelter's Yard with Yacker. The other Wisps escaped Dark Oak and fled with Yacker who promised to send help to Thomas.

"ARGH! WE'RE NOT DONE THOMAS!" Dark Oak chased after him.

"I've already taken care of two of your commanders, you're losing." Thomas said proudly.

"IT'S NOT OVER YET!" Dark Oak promised.

Red Pine was still struggling when he was suddenly let go and he fell to the ground thanks to one of the troopers. Growling, Red Pine ran straight for his terrified troops. After another brawl erupted between Red Pine and his troops they are interrupted by Rouge.

"Should I leave you all to your little catfight?" Rouge smirked.

"ARGH! YOU WON'T STOP ME!" Red Pine said.

"We'll see about that won't we?" Rouge said.

Meanwhile, the Wisps could see Tails and Shade up ahead and hurried to get to them, but unfortunately they were being tailed by Pale Bayleaf.

"Ah, the source of that energy. You all will be coming with me for study!" Bayleaf said.

The wisps flew faster towards the plane with Bayleaf in tow. Bayleaf had already ordered his troops to guard the Narrow Guage Railway and make sure every engines was locked in their sheds. With Black Narcissus, he was busy complaining how about messy the Quarry was. Henry and Mavis were hiding in a shed at another end of the Quarry and have not been spotted, even the trucks remained quiet.

"Hmph, Dark Oak just had to force me to stay here...it sickens me." Narcissus said.

"Black Narcissus, Thomas is coming, be ready!" Dark Oak called.

"Yes sir."

Black Narcissus checked himself out in the mirror on his staff.

"I'm gonna look so good for this." He said.

The gold and silver troopers got ready as well. Thomas speeds into the quarry after a few blocked paths thanks to Dark Oak. Henry and Mavis gasp when they see him. Henry wanted to yell out but didn't want to give him and Mavis away. Thomas saw the tall skinny black metarex and the gold and silver troopers.

"Oh no!" Thomas yelled.

The two troopers lunged at Thomas, but he was redirected into a siding causing the troopers to accidentally tackle Dark Oak out of the sky and onto the ground. Dark Oak angrily threw them off.

"GET OFF ME! STOP HIM!" Dark Oak said.

"With pleasure!" Black Narcissus sneered.

Thomas backed away when Narcissus swung his staff at him. Dark Oak watched from nearby when he heard a sneeze down the line. Henry had accidentally sneezed.

"Henry!" Mavis scowled.

"Sorry." Henry sighed.

Dark Oak decided to investigate while the others dealt with Thomas who was clearly outnumbered. Suddenly, Sonic and Shadow arrive just in time.

"SONIC!" Black Narcissus snarled.

"What? Surprised?" Sonic wagged a finger.

"SONIC!" Thomas cheered.

"We got this, right Shadow?" Sonic said.

Shadow only nodded before they lunged into battle. The hedgehogs took on the two troopers while Narcissus attacked Thomas.

"Come on little engine, show me what ya got!" The commander swung his staff.

"I got nothing to show you." Thomas backed away.

Suddenly Thomas heard Percy's whistle, Percy was racing up behind him with truck full of coal.

"PERCY WATCH OUT!" Thomas yelled.

But it was too late, Percy crashed straight into the back of Thomas knocking him forwards and the trucks broke flinging coal and a cloud of black dust everywhere. Dark Narcissus got caught in it and gasped at his dirty appearance.

"MY ARMOR! YOU ROTTEN MECH!" He roared.

Before Percy could understand what was going on, Narcissus uses all his strength to ram into the side of Percy so hard, he goes tumbling off the rails and barrel-rolls a few feet away crashing into a pile of rocks. Everyone stops...

"PERCY!" Thomas and Sonic yell.

"That takes care of him." Narcissus wiped himself off.

Then they all take notice of Sonic...tears were coming to his eyes. He raced over to Percy who was heavily injured upon impact but alive. Sonic saw his condition...and his mood changed completely. He clenched his fists tightly and a dark blue aura formed around his body. His eyes changed so that they were completely white. His fur becomes black and skin becomes a dark grey. Shadow, Thomas and the Metarex could not believe what they were seeing. It was a shame Dark Oak was distracted right now.

"You...nearly killed him...you...hurt my friend...and now..."

Sonic turned his head and glared at the Metarex.

"I'm gonna kill you..."

Sonic had became...Dark Sonic...

 _ **To be continued...**_


	9. Metarex PT 3

Chapter 9: Metarex PT 3

While one of the workers called the Sodor Search and Rescue Team, the others payed attention to Dark Sonic, Shadow had never seen Sonic this mad, nor did he knew Sonic had this form.

"Sonic...you alright?" Shadow asked.

"I'm...just fine...and I'll be better...AFTER THIS!"

In a flash, Dark Sonic lunged at the gold and silver Metarex and tore them apart and they exploded. Dark Narcissus gasped before Dark Sonic raced towards all the other Metarex troopers in the area. Narcissus decided to hide in Thomas' cab but Shadow appeared behind him.

"CHAOS SPEAR!"

Shadow launched Narcissus out of the cab and onto the ground.

"No...I can't lose like this." Narcissus groaned.

"CHAOS CONTROL!"

Shadow then teleported him and Narcissus under the coal hopper nearby, then Shadow jumped away.

"What? Why did you-"

Shadow then jumped up and pulled a lever unloading all the coal in the hopper and piled onto Narcissus.

"YAH! IT'S SO DIRTY!" Narcissus yelped.

"Hmph, serves him right. Now where did Dark Oak go?" Shadow wondered.

Dark Oak was still looking around for the source of the noise, but he couldn't find anyone. Henry and Mavis remained in the little shed with some trucks in front of them, Mavis had an idea.

"Henry, he's standing on the track and his back towards us. You can ambush him with those trucks." Mavis said.

"I don't know, what if I fail." Henry asked.

"It's still worth a shot."

Henry sighed, Dark Oak just had to be standing on his track didn't he? Oh well. Henry made a dash for the trucks, slammed into them and pushed them towards the Metarex leader. Dark Oak didn't have time to react as he turned around and gets smashed into by the trucks.

"ONWARDS! ONWARDS!" The trucks yelled.

Henry shoved Dark Oak all the way down the track back to the others with Mavis right behind him. Eventually Dark Oak fell back just as the truck ended up derailing, but Henry kept going.

"SURPRISE!" Henry yelled.

"WHAT?" Dark Oak gasped.

Henry rammed himself into Dark Oak and pushed him even further. Then out of nowhere, Dark Sonic kicks Dark Oak in the chest and he goes flying next to the coal-covered Narcissus.

"THOMAS RUN!" Mavis yelled.

Thomas did so, but he took a glare at Percy who still hadn't said anything. He sighed and raced out of the quarry, just as Dark Oak managed to stand up.

"THAT'S IT! NO MERCY!" Dark Oak shouted.

Before Shadow or Dark Sonic could attack, he was already gone. Rocky arrived to finally put Percy back on the tracks. He was dented in a few places and scratched up. Seeing Dark Sonic, Percy gasped.

"Sonic, you alright?" Percy asked.

Dark Sonic saw that Percy was okay now and slowly reverted back to regular Sonic.

"I'm sorry I lost my cool there." Sonic rubbed his head.

"How did you do that?" Shadow asked.

"It's a long story. But it can wait, I'll go after Dark Oak." Sonic said and sped off.

Just then Omega arrives with a knocked out Zelkova and Rouge arrives with a knocked out Red Pine.

"What did we miss?" Rouge asked.

"Sonic apparently has this strange dark version of himself...it's weird." Shadow said.

"Interesting...hey green pea!" Rouge winked at Percy.

"Oh hello Rouge, I'm glad to see you're here to help out." Percy smiled.

Rouge flew up and gave him another kiss on the cheek making him blush while Omega was very confused by the situation but said nothing.

"You two bring those Metarex, I'm going to go find Sonic." Shadow skated off.

In the air, the Wisps, Tails and Shade were busy fighting off Pale Bayleaf.

"I grow tired of this resistance, surrender now!" Bayleaf commanded.

"As if!" Tails snorted.

He continued to fire some blasts at the Metarex who was dodging them all. On the way, Sonic saw a good enough sized hill he could use to leap at Bayleaf.

"TAILS! I'M COMING IN HOT!" Sonic yelled.

He jumped the hill grabbing some major air, Bayleaf didn't see it coming.

"Hope you have a nice fall." Tails said to Bayleaf.

"What do you-"

Sonic's foot to his face cut him off as he spun around in the air, then Yacker used his ship to knock him down using one of the wings and he falls to the ground. Dark Oak sees the commander's descent.

"I guess it's all up to me then, he's proven himself, now he's mine!" Dark Oak said.

Thomas narrowly dodges Bayleaf who crashes onto the track, but Thomas is directed onto another line just in time. Tails and Shade agreed to go towards the Narrow Gauge Railway and take out all Metarex there. Thomas had no idea where he should go now and didn't even stop to ask the others for help when they passed by. Dark Oak caught up and landed on top of Thomas.

"You would make a perfect addition to our army, and there's nothing you can do about it." Dark Oak laughs.

"Sonic will stop you!" Thomas said.

"We'll see about that."

"THOMAS IS RIGHT!" Sonic yelled.

Dark Oak turned to see Sonic racing up beside them.

"UGH SONIC! YOU AGAIN! GET AWAY, HE'S MINE!" Dark Oak snarled.

"You act like he's your child or something, does that make him Cosmo's brother? " Sonic teased.

"SHUT UP!" Dark Oak yelled.

Sonic jumped up to spin-dash Dark Oak but the leader teleported away.

"What, where did he go?"

As he turned around, he's sucker-punched in the face by Dark Oak and knocked into the funnel. Thomas decided to apply his brakes and both Sonic and Dark Oak fly off in front of him. Shadow caught up but didn't have time to create an attack when Dark Oak swung his sword at him quickly making him trip. His chaos emerald flew into Thomas' cab.

"NO! THE EMERALD!" Shadow gasped.

Dark Oak kicked him away and went to retrieve it, Thomas had no idea what to do...but then he remembered all of the different powers Shadow used with it...he decided to try it. As he focused, the emerald glowed a bright green much to Dark Oak's wonder.

"Wait...he's not..."

"CHAOS CONTROL!" Thomas yelled.

Suddenly they all vanished from the area just as Rouge and Omega arrived.

"Did he just..."

"Processor does not compute. Blue machine couldn't have used the power of the chaos emerald." Omega scratched his head.

"I think he just did." Rouge said.

Back at Tidmouth Sheds, Thomas, Dark Oak, Sonic and Shadow arrived and the hedgehogs were in shock...especially Shadow. Dark Oak had to process what just happened.

"Thomas...did you just do Chaos control?" Sonic asked.

"I think so..." Thomas said.

"But you couldn't have, how did you focus so quickly?"

"I remembered how you would do it." Thomas said.

"Wow...that's awesome Thomas. Impressed Shadow?" Sonic smirked.

Shadow shook off his shock and crossed his arms.

"Not bad, for a little engine." Shadow scoffed.

"AS FOR YOU!" Sonic pointed to the Metarex commander.

"I DON'T HAVE TIME TO DEAL WITH YOU TWO! HE'S COMING WITH ME!" Dark Oak said.

"And just how are you gonna do that?" Shadow asked.

Finally Rouge and Omega arrived with Omega looking very exhausted. He of course had to carry all the other commanders back here, then he threw them on the ground.

"Cannot do this...any longer." Omega vented.

"It's alright, after all they're starting to wake up." Rouge said.

The four woke up accidentally slamming their heads together. That's when they noticed Thomas.

"Ah, you actually caught him sir." Pale Bayleaf said.

"Yeah, no thanks to you buffoons." Dark Oak sneered.

"CAN WE SMASH HIM! OR THEM!" Yellow Zelkova pointed at the heroes.

"NO AND NO! WE DON'T HAVE TIME!"

"Leave him alone!" Sonic growled.

Both sides got in a fighting stance but then Tails and Shade arrived and landed next to Thomas and then Yacker and the Wisps arrived in their ship.

"We made it just in time!" Tails said.

"So what's happening here?" Shade asked.

"Your destruction!" Dark Oak growled.

"Actually I have a better plan! How about another race?" Sonic smirked at the leader.

"You mean against you?" Dark Oak asked.

"No, Thomas!"

"This guy? He cheated!" Dark Oak accused Thomas.

"So then it's time for a rematch. If Thomas here can use the power of the chaos emeralds...maybe he can use them to kick your butt all the way to the ARK."

"I'd like to see him try." Dark Oak turned to Thomas.

Thomas felt scared being stared at by the Metarex leaders.

"Sonic, what are you trying to do?" Thomas asked.

"Yeah big blue, what's going on?" Rouge asked.

Sonic then raced into the cab and grabbed the emerald before Dark Oak could lunge.

"Catch us if ya can! Meet us up at the ARK." Sonic said.

"WHAT ARE YOU-"

"CHAOS CONTROL!"

Sonic teleported all except the Metarex up to the ARK leaving the Metarex on Sodor surprised. Dark Oak growled and turned towards the others.

"ALL OF YOU TO YOUR SHIPS! WE'RE HEADING TO THEIR SO-CALLED ARK!" Dark Oak ordered.

"Yes sir." They all saluted.

"At least I managed to salvage my gold and silver troopers." Narcissus sighed.

 _ **Space Colony Ark...**_

When Sonic and co. arrived, they saw they were standing on the upgraded loop circuit that Sonic and Shadow battled on during their first battles and it still looked like the way it was when Sonic was saving his friends from the Time Eater.

"Why did you send us here?" Tails asked.

"I needed to get far enough away from the Metarex in order to see if this choas energy works well on Thomas. Plus, this is the perfect place for one final race against him." Sonic said.

"Fair enough, this place is a lot different then I remember it." Rouge said.

Thomas and the Wisps looked down to see Earth in all it's glory.

"Whoa...I'm actually in space." Thomas smiled.

Yacker and the Wisps were in awe with the setting. Omega felt a little uncomfortable being so high up, and Shade stayed closer to Sonic.

"Don't worry Shade you won't fall." Sonic said.

"I hope not." She said.

Sonic and Shadow then pulled out all seven chaos emeralds.

"You really think this will work? Thomas can only run on rails." Shadow said..

"The emerald's power can do amazing stuff Shadow." Sonic said.

Suddenly the chaos emeralds lifted up by themselves and went to circle around Thomas. He closed his eyes as he felt himself floating off the ground.

"Nnnnnrrrrgghhhh!" Thomas groaned.

"It's actually working." Tails gasped.

Shadow was in such wonder as the emeralds circled around Thomas faster and faster until they went inside him and Thomas' blue paint became yellow, the red lining become blue and both his number 1s becoming black. He was now Super Thomas.

"Whoa, I'm feel all this energy and it's amazing." Super Thomas said.

Just then one of the energy cores flew by.

"Hey that's one of the energy cores, ah good times eh Shadow?" Sonic smiled.

"Good times?" Shadow snorted.

Thomas knew he had to control this energy and think of some way to move, he apparently could float, but what if he wanted to roll on the ground? He closed his eyes and focused as a long line of energy formed underneath him in the shape of railroad tracks and it zoomed out into the distance creating a long stretch of track. It looped around the circuit and came back to the start and connected, much to everyone's surprise.

"Whoa, that was amazing!" Sonic said.

"Hey looks like I can use the rails, even in space." Thomas chuckled.

"Good timing too, here they come!" Shade said.

The Metarex ships were getting closer, mainly Dark Oak's. As they reached the ARK, Dark Oak didn't waste time with leaving his ship and flying straight towards Thomas who gasped.

"YOU'RE GOING DOWN THOMAS! YOU WILL BE PART OF THE METAREX, EVEN IF I HAVE TO REWIRE YOU FROM SCRATCH! AND THEN I'M GOING AFTER THOSE ALIENS!" Dark Oak yelled.

Yacker and the Wisps hid behind Omega just as Dark Oak landed on the track, that's when Dark Oak got a good look at Thomas.

"What happened?" He asked.

"I absorbed all the chaos emeralds, and now I'm more powerful than ever." Thomas smirked.

"WE'LL SEE ABOUT THAT! THIS ENDS NOW!" Dark Oak shouted.

As another energy core raced by, Dark Oak raced ahead and Thomas blasted forwards with Sonic and the others behind him.

"GO GET HIM THOMAS!" Sonic shouted.

"YOU'VE GOT THIS THOMAS!" Shadow said.

"Really?"

And so Thomas and Dark Oak raced each other for the energy core expecting to get powered-up even more. Sonic, Shadow and the Wisps were ready to assist in anyway they could.

"YOU'LL NEVER BEAT ME THIS TIME THOMAS!" Dark Oak yelled.

"I'M DOING THIS FOR THE ISLAND OF SODOR AND MY FRIENDS! I WILL NOT ALLOW HARM TO COME TO THEM!" Thomas yelled.

Thomas' blue aura and Dark Oak's purple aura clashed when Dark Oak tried to ram Thomas off the energy rails but Thomas was much more durable then that now. Dark Oak tried to cut him with his sword but Thomas found himself about to tip the opposite way to avoid the swipe. Thomas never thought he could go as such speeds, he'd have to tell Gordon later.

"CHAOS SPEAR!" Thomas shouted.

Some energy spears fired out of his funnel and hit Dark Oak knocking him away.

"ARGH! WHY YOU!" Dark Oak growled.

The continued to race around the bends and boost through straightaway as the first core was coming up fast.

"IT'S MINE!" Dark Oak yelled.

He sped up a bit more and absorbed it before Thomas could and felt a greater burst of energy. He managed to get farther ahead before turning around. His sharp claws spewing electricity from the ends.

"FEAR THE METAREX!" Dark Oak shouted.

He started to shoot several sparks of electricity from his claws and tried to zap Thomas. As Super Thomas, he had the ability to change the shape of the tracks he created and made the tracks curve around the blasts. Getting angrier, Dark Oak fired one last ball of electricity before his new energy died out. Thomas swerved out of the way and boosted ahead of Dark Oak knocking him over.

"ARGH! YOU'RE FINISHED!" Dark Oak yelled.

"WOW! Thomas knows how to use it well!" Sonic said.

"It's very impressive." Rouge said.

"What amazing power." Tails said.

"Maybe he's not as inferior as I thought." Omega said.

"What do you think Shadow?" Shade asked.

"Hmph...beginner's luck." Shadow scoffed.

Rouge rolled her eyes knowing he was lying and was secretly impressed. Dark Oak tried more times to knock Thomas off the rails but the rails would simply catch him if he fell over and put him back straight.

"HOW CAN YOU DO ALL THIS? YOU'RE JUST A LITTLE TANK ENGINE!" Dark Oak roared.

"Little engines can do big things...CHAOS BLAST!"

A wave of energy knocked Dark Oak to the ground and he tumbled into the distance just missing the energy core, Thomas managed to get the energy core first.

"NO!" Dark Oak yelled.

Thomas felt even more energy surround him and grinned wildly at Oak.

"Oh no!" Dark Oak said.

He tried to fly away but up ahead some meteors were blocking Thomas' way and Thomas decided to ram them. With his upgraded speed and strength, he bashed the meteors into Dark Oak about 12 times, having to curve the track so he could hit them directly. After the final hit, Dark Oak couldn't take anymore and is flung into the air and crashed hard onto the ground finally defeated. Thomas and the others stop in front of him. Dark Oak was sparking everywhere and struggled to get up.

"No...I can't lose to you." Dark Oak said.

"You just did." Thomas smiled and whistled.

The other four commanders arrived as well.

"Hmph, great plan Dark Oak. You lost to a little machine!" Red Pine said.

"He tried." Yellow Zelkova shrugged.

"But failed." Pale Bayleaf sighed.

"Ugh...this coal is disgusting. I hope it doesn't take so long rebuilding the gold and silver troopers." Black Narcissus whined.

Dark Oak finally got up and growled as Thomas reverted back to normal and the emeralds landed in Sonic's hands.

"Looks like you're not just a little blue machine after all. In fact, you may just be one of the most powerful in the galaxy. I just can't believe the Metarex...lost to you." Dark Oak said.

"Just remember all this next time you try to take over the island." Thomas said.

"Hmph, we don't have plans for that. But know this...we'll be back...not for you, but to finally defeat Sonic the Hedgehog and take over this wretched galaxy." Dark Oak swore.

"Pfft, I'll be waiting." Sonic held a thumbs up.

With one final glare to Thomas, the Metarex teleported to their owns ships and went to the mothership leaving for good. Rouge poked Shadow on the shoulder.

"I believe someone here has something to say to Thomas." Rouge said.

Shadow looked away...he hated to admit stuff. But giving in, he sighed and walked over to Thomas.

"Thomas, that was some...fine work...I'm impressed with your skills to control the emeralds." Shadow said.

"Thanks Shadow, that means a lot." Thomas smiled.

"Aw that's so cute Shadow." Sonic teased.

Shadow gave Sonic a death glare before chaos blasting him away.

"Shut up...faker..."

 _ **End of ARC 4.**_

 _ **To be continued in the final arc, ARC 5: Rise of Lyric...**_


	10. Lyric PT 1

**_Finally we've reached the final arc of this story and I've had fun writing this! And so I'm hoping to end this story with hope that I've created a successful story. Just like the Metarex, for this story I made Lyric exist in the main game universe instead of Boom. Enjoy!_**

* * *

ARC 5: Rise of Lyric

Chapter 10: Lyric PT 1

Awhile after Thomas used the power of the chaos emeralds and sent the Metarex packing, they had all got back to the Island of Sodor where all traces of Metarex troopers were destroyed since their bodies exploded when the heroes defeated them. Team Dark had decided to leave and Shadow kept the green chaos emerald. Sonic decided to keep all but the blue emerald and left it with Thomas. The next morning, Tails had some more work to do with rebuilding the tower without Wave's help. Little did they know, one final threat will soon rip the brief peace on Sodor with his metal claws.

Sonic, Tails, Shade and the Wisps agreed to stay on the island...though Sonic and Tails needed to check on things back in Station Square soon. The Wisps even started to help the engines with their jobs, Shade often talked with Percy when Thomas wasn't around and Sonic raced around the island for fun. Unfortunately the new threat was already on the Island...waiting...lurking...studying.

"So Tails, is it almost finished?" Sonic asked as he raced over.

"Just about done Sonic, I guess after this we'll be going home." Tails said.

"Yeah, I'm starting to miss it, but this place is like a paradise. We've got to come here more often, but it would be best to head home in case Egghead has something planned for us to destroy." Sonic said.

"I won't be surprised." Tails chuckled.

"What about you Yacker, you guys heading out too?" Sonic asked.

Yacker shook his head and made a few expressive gestures and Tails looked on his translator.

"He said not yet, they're loving the island and don't plan on leaving any time soon." Tails read out loud.

"I don't blame ya, this place is epic! Even though we've had to fight a few people." Sonic smirked.

Just then Sir Topham Hatt arrived and tipped his hat towards the mobians. All the engines began to wake up.

"Hello Sonic and Tails." He greeted.

"Hello sir, all those Metarex have been defeated. You should've seen Thomas, he used the powers of all the chaos emeralds and became Super Thomas, he raced the leader through space and basically banished them from the Island." Tails explained.

All the engines were shocked by this info and Thomas blushed.

"I wasn't going to let this island fall." Thomas said.

"You were awesome Thomas, one of the bravest people I know." Sonic said.

"Thanks Sonic!" Thomas smiled.

"Hey Thomas, you should show them those abilities." Sonic said.

"Okay I'll try...CHAOS CONTROL!"

Thomas suddenly vanishes in front of everyone and they all gasp.

"He's gone!" Edward yelped.

"But where?" Henry asked.

Then Thomas appears on the turntable and backs up into his shed.

"Whoa." Gordon said.

"That's incredible." Emily said.

"Very interesting." James said.

"Thomas...what else can you do?' Percy asked.

"CHAOS SPEAR!"

Some spears shot out of his funnel and landed near Sonic who jumped back.

"Whoa watch it there, by the way I wouldn't use Chaos Blast unless you want to destroy the sheds." Sonic smirked.

"No thank you." Thomas chuckled.

Just then, Shade came out of Percy's cab yawning.

"Morning engines, Sonic, Tails, Sir..." Shade came over.

"How'd you sleep?" Sonic asked.

"Pretty good actually." Shade smiled.

"So you staying here for awhile?" Tails asked.

"Now that all those threats are gone, I can finally relax for awhile." Shade said.

"Good, but me and Tails need to head back...if that's okay." Sonic said.

"It sure is...it was nice fighting by your side." Shade shook their hands.

"Same here." Tails said.

Yacker asked for a high-five from them.

"Right on!" Sonic said.

He jumped up and high-fived Yacker and Tails did the same. Later on after saying goodbye to the engines, Sonic and Tails had finally left the island leaving Shade and the Wisps. Sir Topham Hatt turned to the engines.

"Engines, due to more damage around the island, some places will be closed off until repairs can be done. Thankfully it wasn't a heavy toll, and it's only a few places. I've decided to close down the Smelter's Yard, a small part of the Quarry, Wellsworth Sation and unfortunately Thomas' branch line." He explained.

"Aw." Thomas sighed.

"Don't worry Thomas, surely it will be one of the first places fixed." Percy said.

"Indeed it will, we just need time Thomas." STH said.

"Yes sir." Thomas said.

"As for the rest of you, Gordon you have the express to pull, Henry, a goods train is waiting for you at the docks, and Emily your coaches are waiting. That is all!" STH ordered.

"Ah, finally the express." Gordon whistled.

"No boasting Gordon, after all, the Wisps will be helping you!" Thomas teased.

Gordon groaned not wanting to remember when the Wisps used the engines for their own amusement.

"Well I'm going for a wash!" James puffed away.

"Hmm..." Edward thought.

"What's wrong Edward?" Henry asked.

"I don't know...something feels wrong." Edward said.

"Just think positive Edward." Henry said as he left.

"So what do you want to do Yacker?" Percy asked.

Yacker looked over to the pink wisp who zoomed straight for Percy and absorbed him.

"I see where this is going." Shade chuckled.

SPIKES!

Percy turned into a spike ball and blasted off into the distance. Shade laughed not noticing the cyan wisp coming towards her and absorbed her.

LAZER!

Shade turned into a ball of energy that zoomed away leaving the other Wisps laughing.

"Never turn your back on a Wisp." Yacker shrugged.

One month later, things were almost back to normal on the Island, but suspicions and worry still plagued the Island. Some people have noticed strange tall circular buildings made of black metal with red outlines and circuits all over the place. Many have heard rumors of a creature lurking around the Smelter's Yard but no one dared go near it...plus it was still on the schedule for rebuilding...but it didn't need rebuilding anymore. More and more black and red towers started to appear close to that area and the ground itself was starting to become all metal. The Smelter's Yard definitely wasn't going to be the same again.

One night, Percy and Shade were asleep while the Wisps were sleeping the ship next to the sheds. Henry was the only one gone to pull the Flying Kipper while the others remained asleep. Unknown to them, a large strange figure was lurking around the sheds. It looked like snake with robots parts built all around it. The figure floated inside the sheds and stayed behind the engines seemingly examining them and making comments.

"Hmm, nothing too big...nothing too old...nothing that will stand out...oh...what have we here?"

The figure stopped behind Thomas and examined him, he felt a strange energy from him, but he couldn't see the blue chaos emerald inside Thomas' empty fireplace.

"Very interesting...I'll keep him in mind."

Then he turned to Percy and his eyes seemed to be flash with surprise.

"Ah...he looks pretty young...probably a bit naive as well...he'll do."

Completely oblivious to the sleeping Shade, the figure proceeds to float out of the sheds while purposely swiping Percy's face with the claws on his tail. This woke Percy up and he looked around.

"What? Who...huh?"

Percy could make out some eyes glowing in the pitch black darkness and a pearly white but sharp set of teeth form a grin, then they disappear quickly. Percy gasped and was very confused to what he just saw...and he was afraid.

"What was that?" Percy gasped.

He accidentally awoke Thomas who kept his eyes closed.

"What's wrong Percy?" Thomas asked.

"I thought I saw someone staring at me...he looked evil." Percy whimpered.

"Ah I'm sure it was just a dream, besides we haven't had anyone attack the island for a whole month." Thomas said.

"Yeah, I guess you're right." Percy said doubtfully.

The next morning, Percy was still thinking about what he saw and explained it to Shade.

"That is strange, I don't think you were imagining it Percy. At least he didn't spot me or the chaos emerald." Shade said holding it.

"Well I doubt Thomas will go Super Thomas again since Sonic had most of them and Shadow has one." Percy said.

Thomas heard him and chuckled.

"I'm sure I only needed it that one time. Besides, if we any need power, we have the Wisps." Thomas said.

"Until they leave." Percy sighed.

"True. So you still think what you saw was real?" Thomas asked.

"Of course, strangest thing was...the tower didn't go off."

"Maybe he's a good guy."

"Not after that stare I saw. He must be resistant to it or something."

"Possibly, anyways I have to do some jobs on my branch line, I'm just glad it's open again." Thomas smiled.

"Alright then, me and Shade are gonna investigate." Percy said.

After Shade placed the chaos emerald back in Thomas' cab, the two whistled and went their separate ways. When Thomas collected Annie and Clarabel and raced onto his branch line, they couldn't help but feel they were being watched.

"Annie, Clarabel, do you see anyone else around?" Thomas asked.

"No Thomas, no one but us." Annie said.

"Why do you ask?" Clarabel asked.

"Oh nevermind, I'm just being paranoid again." Thomas chuckled.

"It's been a while since that happened. Last time you were paranoid, there was actually a threat, maybe there's a new threat coming." Annie said.

"Oh don't worry Clarabel, our dear Thomas can handle himself, especially after what happened a month ago." Clarabel reminded her.

"True."

When they passed by a tall tree, they didn't see the strange figure again lurking behind and staring at him. After dropping off some passengers, Thomas ventured away from his branch line and towards the docks where Salty and Cranky were hard at work.

"Arr, ahoy Thomas. What brings ya here?" Salty asked.

"Well, I felt like I was being watched...Percy mentioned some strange evil creature spying on him last night and he's gone out to find it...and I'm starting to believe him." Thomas said.

"Strange creature you say? Did Percy describe it?"

"He said he didn't get a good look, just saw a pair of eyes and mouth full of sharp teeth." Thomas said.

"Ooh that's creepy indeed. But I don't think I can help ya! HEY CRANKY!"

"What?" Cranky said turning to him.

"Have you seen anything strange in the sky or maybe someone lurking around?" Salty asked.

"Nope, too busy." Cranky said going to pick up another large box.

Just then Edward arrived to pick up the flatbeds that Cranky was loading.

"Hello Thomas and Salty." Edward said.

"Ahoy Edward!"

"Hello Edward, no time to talk, I need to locate this strange spy." Thomas puffed away.

Leaving the docks, Annie and Clarabel were starting to have doubts about what Percy had saw.

"I really don't think Percy saw anything, he had to be dreaming." Annie said.

Suddenly there was a loud explosion, like lightning had struck something.

"Whoa, what was that? Let's go find out!"

Thomas arrived at the windmill and gasped when he saw it was completely destroyed. Blade pieces were all over the ground, luckily no one was hurt.

"Oh dear, the windmill!" Thomas gasped.

Thomas started to wonder who could've done something like this. Meanwhile, Percy and Shade were continuing to search around for anything wrong.

"Still nothing. He has to be here for sure." Percy said.

"We should check any closed off areas that were under reconstruction." Shade suggested.

"The only place still closed is the Smelter's Yard, let's check there." Percy said.

Shade looked up and saw something strange.

"Percy, has the tower always been there?" Shade pointed.

Percy saw a large black and red tower that was a far in the distance.

"No, I've never seen it...hey...there's another."

Shade saw another spiky-like tower even further away.

"We should follow them." Shade said.

And so they kept getting closer and closer to the towers until they found themselves heading towards something out of the usual. Percy screeched to a stop and saw that the ground was completely metal and the rails had turned red.

"Whoa this is new, did they upgrade the Smelter's Yard?" Percy asked.

"This isn't good, but we need to find out more info." Shade said.

Percy nervously moved forward onto the red glowing rails and continued closer to the Smelter's Yard. There were no signs that said it was under construction, and there were no humans around. Then came the craziest surprise to him. More and more circular towers, and strange machines and pipes covered the area, he went towards an area that seemed like some kind of arena with pieces of scrap lined around creating a circular barrier. But the tracks were clear and Percy kept going.

"Be brave Percy, we must find out what's going on!" Shade said.

"This doesn't look like the Smelter's at all." Percy gulped.

He looked at all of the strange pipes that were all above him going in different directions, piles of scrap neatly placed around the edges of the area, the buildings looked like storage facilities, all computer terminals, automatic doors and much more. The deeper they entered, the more deep and small they felt.

"How long has all this been here? It's only been a month." Percy gasped.

"You can do a lot in a month, especially when you're not interrupted." Shade said.

Suddenly they were stopped immediately. Percy looked down to see they were now on a platform, it began to move forwards away from the track, they went even deeper into the area and it started to get pretty packed. Some red smoke blasted everywhere and loud humming from machines could be heard. Percy then gasped when he saw some strange small robots doing stuff on most of the computer terminals.

"Whoa...where did they come from?" Percy asked.

"Get ready, I think we're approaching the end." Shade said.

They came towards the final automatic doors that looked like the ones to enter the Smelters. Percy saw the familiar red mist that covered the inside and figured the building was okay after all, but when they got inside, they saw it completely changed. Inside it was rather clean, the claw above was up higher, the machines were upgraded and the track was gone, Percy remained on the floating platform. That's when he and Shade heard evil laughter. Out of the thick red mist ahead, came the figure Percy saw last night. Getting a better look, he saw that the figure was a large snake in robot armor, a claw attached to his tail and had big arms with sharp claws on the end for hands.

"Well well well, a little curious are we?" The figure snickered.

Percy almost had no words as the snake came closer and towered over him.

"Who are you? What have you done to the Smelters?" Percy asked.

"I'm am Lyric, and I've upgraded this place to my specifications, consider it my 2nd base of operations." Lyric said as his tongue slipped out and in.

Lyric leaned down to Percy's face and gave him the same look he did last night.

"Surprised to see me in person?" Lyric asked.

"Yes...why were you spying on us?" Percy asked.

"I plan to rid this planet of all plant and animal life and build my robotic empire. But while I've already collected the crystal fragments I needed to power up my main machine, I'm am in the middle of requesting mandatory help. I'm seeking new allies that will serve me without question and help me destroy this place, I'll turn them into full-on clones and they'll have no choice but to do by bidding." Lyric explained.

Percy gasped...this was very bad.

"So...why us? And how long have you been here?" Percy asked.

"So many questions, not to worry, you deserve to know. I've decided to start out small, and your island seemed like the perfect place to start and destroy just for me to rebuild it piece by robotic piece. Besides, you should all join me, you all are basically robots as well...you almost rule this island...yet you choose to live equally with those wretched fleshbags. Not to worry, I picked you and the little blue one out for a reason. You see, I've been here the whole time since that robotic doppelganger came. I was lucky enough to bypass any detection of me here and hide until all the threats were gone. I've seen everything, him, the knights, those aliens, and even those pathetic Metarex. None of them are as powerful as me! And it was during those time that I learned a lot about you and other one...Thomas is it? I was very impressed by his amazing abilities...and I can just think of the power I could have with all the chaos emeralds and the Wisps...I'D BE INVINCIBLE!" Lyric yelled.

"Not if I have anything to say about it." Shade came out of the cab.

"Ah, you brought a guest...how interesting."

Shade wasted no time trying to jump at him, but was tackled down by a few minions.

"Minions, tie her up, I have business to accomplish with him." Lyric pointed a claw at Percy.

"LET ME GO! PERCY!" Shade yelled.

One of the minions then knocks her out and drag her into a small empty back room. Lyric turned back to Percy and towered over him, his claws snapping and electricity flowing around them. Percy thought this was the end for him.

"Now then Percy, I'm going to make you my first recruit." Lyric snarled.

"No! Never! I won't do it!" Percy snapped.

"Ah but you will after I do THIS!"

Lyric grabbed one of his mind control devices and clamped it down on his funnel. Percy fought the control for a brief moment but then he made a blank stare.

"What is your wish master?" Percy asked in a robotic voice.

"Fetch me...Thomas the Tank Engine..."

 _ **To be continued...**_


	11. Lyric PT 2

_**And now this will be the final chapter of the story! I was so excited to write this story at the start but I've been postponing it constantly after doing other stories first! But now it's here and at the end already, well, all I can say is enjoy!**_

* * *

Chapter 11: Lyric PT 2

Later that day, Thomas arrived at Knapford Station where Gordon was just about to leave with the express. Thomas had to whistle to get Gordon's attention.

"Gordon, did you see the windmill? It's been destroyed!" Thomas told him.

"What? Who did it?" Gordon asked.

"I don't know...but it's very strange, it was like it was struck by lightning." Thomas said.

"Hmm, well I don't have time to deal with it now. The express awaits!" Gordon toots his whistle.

As Gordon left, Sir Topham Hatt arrived.

"Hello Thomas, what are you doing here?" He asked.

"Hello sir, I went by the windmill and it was destroyed, something must have struck it. But I don't know how that could've happened." Thomas said.

"Oh dear, we'd better be careful then, maybe a new threat has arrived. We can't keep having these on my railway." STH shook his head.

"I agree, whatever it is, I'll make sure they leave." Thomas said determined.

"That's good Thomas, just be aware at all times."

"Yes sir."

Thomas chuffed away to do other things, he along with everyone else unaware that slowly the island was being consumed by black and red metal, more buildings began to rise up and houses and business became more futuristic looking. The sky above the Smelter's started to become red. As Thomas raced along the line with Annie and Clarabel, they were about to recieve an unexpected guest. Clarabel could see Percy coming towards them.

"I say it's Percy, but he looks...different." Clarabel said.

"Different? What do you mean?" Annie asked.

"He has some strange device on his head...and his eyes are red...AND HE'S COMING STRAIGHT FOR US!" Clarabel asked.

"What!" Thomas gasped.

"GET THOMAS!" Percy yelled.

"THOMAS RUN!" Annie yelled.

And so Thomas raced as fast as he could away from Percy, luckily Thomas was faster than Percy. Percy chased Thomas around a few bends, past a few engines and eventually found the Dieselworks.

"Maybe I could hide there!" Thomas thought.

"Clarabel is he gaining on us?" Annie asked.

"He's far behind, but we better find somewhere to hide fast!" Clarabel said.

"I know where!" Thomas said.

He raced into the Dieselworks and fled into a siding that had towering pieces of scrap. He remained silent as he heard chugging.

"COME OUT THOMAS! YOU'RE JUST DELAYING THE INEVITABLE! LYRIC WILL RULE THIS ISLAND!" Percy said.

"Lyric? He must be the new threat." Thomas thought.

They remained silent until Percy chuffed away and out of sight. Thomas sighed with relief until Diesel spotted him.

"Thomas? What are you doing?" Diesel asked.

"Oh, I was hiding from Percy." Thomas said backing out of the siding to face Diesel.

"We don't need any of that foolishness around here." Diesel sneered.

"No you don't understand, Percy is not himself, apparently there's this guy named Lyric who's invaded this island. I think he has Percy under his control, we have to stop him." Thomas said.

"And what could we possibly do? You don't have all of those Chaos emeralds this time, and Sonic is gone." Diesel said.

"True, but Shade and the Wisps aren't. I just need to find them." Thomas said.

"Well uh...good luck I suppose." Diesel said rather uneasy.

"Uh thanks...huh?"

They both look down as the ground beneath them turned into metal, the piles of scrap melting down and more industrialized buildings popped up. The Dieselworks itself looked more modernized but the Diesels themselves had managed to escape before the transformation. Diesel 10 with his repaired claw came over.

"What's going on?" Diesel 10 snapping his claw in anger.

"It has to be the work of Lyric. I'll find him!" Thomas whistled.

He backed out of the Dieselworks, making sure Percy wasn't there and left back to Tidmouth Sheds where he thought the Wisps would still be. Meanwhile, over at Lyrics's new lair AKA the upgraded Smelters, Lyric was interrogating Shade who was refusing to answer anything.

"FOR THE LAST TIME...WHERE IS SONIC? AND WHERE ARE THOSE ALIENS!" Lyric snarled.

He had Shade trapped in his tail claws and was slowly squeezing her.

"I'M NOT TELLING YOU! YOU WON'T GET AWAY WITH THIS!" Shade yelled.

Lyric roared and tossed Shade into a wall. She struggled to get back up and glared at him.

"I'LL FIND OUT EVERYTHING! YOU THINK YOU'RE SO TOUGH HUH?"

"I'm one of the toughest ones out there...Sonic knows it, they all do." Shade said.

She got back on her feet and Lyric motioned for her to come at him. Shade put on her helmet, got out her blades and jumped to slash at him, Lyric swung his claws but then Shade warped away.

"HUH?"

Then Shade appeared up higher and slashed Lyric's helmet making a long mark.

"AUGH! YOU'RE LUCKY I DON'T HAVE TO SEE THROUGH THAT!" Lyric yelled.

He whacked her away with an arm, but Shade bounced off the wall and tried to stab him in tail but Lyric dodged out of the way. Shade landed to the ground and turned, only to get sucker-punched back in the wall. She lands on the ground hard...but her armor allowed her to not feel so much damage.

"Ugh...I can't beat him alone. I hope the others are okay, I need to contact Sonic." Shade said.

"Are you finished already? Are you gonna tell me what I want to know, after all, Percy will be back with Thomas any minute now and then I'll have him capture those aliens!" Lyric chuckled.

"ARGH! I WON'T LET THAT HAPPEN!"

"WE'LL SEE ABOUT THAT!"

Lyric and Shade lunged at each other, meanwhile Thomas was facing problems of his own, not only did he not know where Percy was...but he was running out of water, and there was no water tower in sight.

"This isn't good." Thomas gulped.

"Faster Thomas, we have to get to the sheds." Annie said.

"I don't see Percy anywhere yet." Clarabel said.

"Good, hey there's Toby!"

Toby was trundling along with Henrietta when they saw Thomas.

"Hello Thomas, what's the rush?" Toby asked.

"I have to get to the sheds to find the Wisps." Thomas said.

Suddenly the metal ground caught up with them and it covered the while area in metal buildings and red glowing railroad tracks. The trees and bushes died and sunk into the ground.

"Oh no, it's too late!" Thomas said.

"What is? What's happening?" Toby asked.

"The rise of Lyric." Came a voice.

Thomas gasped when Percy came in front of him laughing evilly.

"PERCY! PLEASE STOP! WHY ARE YOU DOING THIS?" Thomas asked.

"Boss' orders!" Percy said.

Thomas noticed the mind control device on Percy's head and gasped.

"No...you're being brainwashed Percy."

"Pah, you're just trying to get out of this situation. Now then, you're coming with me to Lyric's lab, he wants to speak to you." Percy came closer.

Toby wanted to do something, but he was on another line. Thomas tried to move, but to his shock, all his water had run out. Seeing his chance, Percy puffed straight into Thomas, his evil red eyes staring into Thomas' horrified ones.

"Let's move!" Percy said.

Thomas found himself uncoupled from Annie and Clarabel who gasped.

"THOMAS!" Annie and Clarabel yelled.

"THOMAS!" Toby yelled.

Percy pulled Thomas away from them quickly, but Toby wasn't going to let them get away.

"Henrietta stay here, I must go after them." Toby said.

"Oh you're so brave Toby!" Henrietta said.

And so Toby chased Thomas and Percy, and eventually other began to join in. They passed by James who was traveling and he joined in, Henry and Edward were talking at a station and saw the scene and joined in, Gordon was napping after pulling the express and joined in. Soon the whole group was chasing after the duo across the island.

 _ **Station Square...**_

Sonic and Tails were out on a walk with Knuckles who getting some food to take with him back to guarding the Master Emerald. Currently they were all eating ice cream.

"So I finally got that portal finished, now we don't have to keep taking the Tornado-2 to the island." Tails said.

"Sweet, I wonder how they are doing?" Sonic wondered.

"Next time you guys go, I should come with. Especially if there's robots to smash." Knuckles said.

"Sure why not." Sonic shrugged.

"I hope nothing bad has happened yet." Tails worried.

"I'm sure they're fine, what could go wrong?" Sonic said.

Suddenly they heard some static on the communicator Sonic was still wearing.

"Huh? There's some interference." Sonic said.

 **"SONIC...SONIC ARE YOU THERE...?"**

"Shade? What's wrong?" Sonic asked ignoring his melting ice cream.

 **"I NEED HELP! THE ISLAND IS IN...DANGER...YOU NEED...TO...HELP!"**

"We'll be there soon!"

"Sonic what's wrong?" Tails asked.

"It's Shade, apparently someone actually managed to bypass the tower, we need to get over there now!" Sonic said.

"Count me in!" Knuckles said.

"Come on!" Tails said.

Over at G.U.N. HQ, Omega was walking along the halls bored, he'd already destroyed every target in the practice room and had nothing to do. Shadow and Rouge were gone for now but Shadow had left the chaos emerald. He found it in a storage room and picked up. Secretly he had been wanting to try out Chaos Control ever since he saw Thomas use the emeralds to take out the Metarex.

"Surely even someone like me can use it." Omega figured.

Deciding to get out of the room, he focused on the emerald.

"I can do this...CHAOS CONTROL!"

Omega vanished from the room, and ended up high in the air. Quickly cutting on his boosters, he flew triumphantly around.

"Even a robot as superior as me can use this." Omega said.

Just then he saw Sonic, Tails and Knuckles racing into Tails' workshop.

"I can't believe that Island is under attack again!" Sonic said.

Omega figured they were talking about Sodor...he still hadn't had his rematch with Thomas...and figured this was his chance. But before he could fly down, he was rammed into from the side, the emerald leaving his claws...and into the claws of another robot.

"YOU!" Omega pointed out.

The emerald was now in possession of Metal Sonic who looked at it.

"I can use this to go back to the island, I wanted to see them again...and I will." Metal Sonic snarled at Omega.

Omega flew at Metal and they grappled for the emerald, their little scuffle ended up making them dive towards Tails' workshop just as the fox got the portal opened. Tails scanned the monitors.

"It looks like some strange plague of metal has taken over the Island...it looks like-"

"Aha! This has to be the work of Lyric, I thought that guy gave up and retreated a long time ago...he's been busy." Sonic said.

"Well what are we waiting for, robots to fall out of the sky?" Knuckles asked.

Suddenly Omega and Metal come crashing in, the force causes Knuckles to go flying into Tails who had just grabbed his translator and they both go flying into the portal. The emerald lands in Sonic's hands...he gasped.

"Uh-oh."

He gets no time to react when Omega and Metal tackle him through the portal.

 **Sodor...**

The Wisps had followed the engines all the way to the Smelters where Lyric was busy making sure the central machine by the large arena was working properly, almost half of Sodor was covered in futuristic metal and machinery. No one was safe anymore...especially the engines. One of the robots had managed to kidnap Sir Topham Hatt and lock him in the back room with Shade who was bruised everywhere and bleeding from her mouth...she had lost her battle. Percy, Thomas and the other engines arrived to find Lyric floating in the air and laughing.

"HAHAHAHAHA...you've done well Percy...very good." Lyric snapped his claws.

"Thank you master...Thomas is all yours." Percy went onto another line.

Thomas gulped as Lyric floated down to face him, his evil grin growing bigger.

"So...Thomas the tank engine...I've been expecting you. I've seen all that you've accomplished, and I must say I'm impressed. And I'll be even more pleased when you're working under my rule...as for your friends..."

Lyric pressed the blue button on his armor and wherever the other engines were, they were lifted up onto their own platforms and raised high in the air, then they were covered by a force field.

"AAAHHHH!" Edward screamed.

"We're too high up!" Henry shut his eyes.

"I don't like this at all!" James whimpered.

"Thomas you have to save us." Toby yelled.

"HELP THOMAS!" Gordon yelled.

Thomas had no idea what to do, the Wisps finally arrived but were quickly spotted.

"And the aliens have arrived, how delightful."

Lyric pressed the button again and the Wisps were trapped in a large bubble that came out of the ground.

"NO!" Thomas yelled.

"Quiet you!" Percy sneered.

"Now then...let's talk about this in a more private location." Lyric said.

Thomas and Percy ended up on their own platforms with the Wisps staying with Thomas. They moved deeper into the area while the others stayed behind in worry. Meanwhile, Sonic, Tails, Knuckles, Metal and Omega landed by the damaged Windmill.

"ALRIGHT METAL, IT'S TIME FOR ANOTHER FIGHT!" Knuckles clenched his fists.

"NO! I'M HERE TO SEE THOMAS AND PERCY!" Metal yelled back.

"What?" Sonic was confused.

"That's why I was here before...to escape you and I found this place...it's relaxing." Metal looked off into the distance.

"Well they're in danger...look at this place." Tails said.

They all examined the island which didn't look like the Island.

"I scanned the island, they're trapped over there and by what they called, the Smelter's Yard!" Omega pointed out.

Sonic nodded and looked at Metal who stared back...it seemed intense. Then Sonic held out a hand.

"Truce? Until the Island is saved?" Sonic said.

Metal seemed hesitant...but he wanted his friends to be safe. He shook Sonic's hand.

"Truce." Metal nodded.

"LET'S GO!" Sonic yelled.

Percy and Thomas had finally arrived at the arena-like area and Lyric chuckled.

"Now that we're alone, it's time for your transformation Thomas, and trust me, it's gonna hurt...A LOT!" Lyric sneered.

"Hmph, you'll never win!" Thomas retorted.

Lyric growled and got in Thomas' face.

"When will you accept that you're defeated this time! The Island is under my command now! I OWN THIS ISLAND! YOU DON'T! I HAVE THE FAT CONTROLLER AND THAT ECHIDNA! YOU'RE FINISHED! WHY CAN'T YOU JUST ACCEPT THAT?"

"BECAUSE YOU'RE WRONG!" Came a voice.

Lyric looked the wrong way and from the other direction, Sonic appeared and homing attacked him out of the sky.

"SONIC!" Thomas beamed.

The Wisps cheered as Sonic and the others landed on the ground and he gave a thumbs up.

"S'up guys, long time no see. Now then, what's happened here?" Sonic asked.

"Lyric captured my friends back there, and brainwashed Percy into bringing me here. And Shade and Sir Topham Hatt are captured inside the Smelters."

"Got it, Tails go and shut off the machine that has the engines captured, Metal go and rescue Shade and Sir Topham Hatt, Omega you go-"

Sonic didn't finish when he saw Omega and Lyric locked in a vicious fist-fight.

"Uh...nevermind, Knuckles we got some smashing to do! Take out all these robots and free the Wisps." Sonic said.

"ALRIGHT! I'M LOVING THIS ISLAND ALREADY!" Knuckles shouted.

Tails flew towards the entrance and found the engines all trapped in the air.

"I got you guys!" Tails said.

He saw a few robots advancing on him and he grabbed a large pipe and starting swinging wildly. The engines watched with wonder as Tails managed to destroy the robots and finally destroyed the machine trapping the engines. They lowered to the ground.

"Thank you Tails!" James said.

"No problem, I suggest you all evacuate now. We got this covered, unless one of you would like to help." Tails shrugged.

"I will." Toby said.

And so the other engines left out of the area while Tails and Toby went back inside. Metal destroyed several more robots as he managed to get inside the Smelter's, dodging the claw that fell down and crashed into the back storage room where Shade and STH were talking.

"Huh? Metal?" STH gasped.

Shade had never seen him before, but figured he was trying to rescue them. Metal put them under his arms and raced out of the Smelters to take them to safety. With Thomas, he was trying to persuade Percy to resist the mind control.

"Percy please, we're friends! You don't want to do this." Thomas said.

"I ONLY LISTEN TO MY MASTER!" Percy snarled.

Then he charged Thomas, but thankfully, Knuckles jumped in between and smashed the mind control device and Percy went back to normal, the punch was strong enough to stop him from crashing as well.

"Thomas? What happened?" Percy asked.

"Percy you're okay! Lyric brainwashed you!" Thomas said.

"Oh, hey what's going on?" Percy asked.

"Sonic is back with the others and we're helping to stop Lyric." Thomas informed him.

"It's going well so far." Knuckles chuckled.

"Who are you?" Percy asked.

"The name's Knuckles!" He smirked.

"Why is it that?"

"You're about to see."

Two robots came at him and Knuckles jumped at them and punched them both through the chests and they exploded.

"Whoa!" Percy gasped.

"Impressed huh?" Knuckles said.

Toby and Tails arrive.

"Everyone's safe and Toby wanted to help...where's that machine to free the Wisps.

Sonic then spin-dashed into a panel nearby and the Wisps were free. Yacker hugged Sonic.

"Glad you're safe Yacker." Sonic chuckled.

Metal arrived with Shade and STH.

"SIR! SHADE!" Thomas gasped.

"Are you okay?" Knuckles ran over to her.

"Hello Knuckles and yes I'm fine." Shade nodded.

But then she collapses to the ground revealing her lie. Tails and Sir Topham Hatt agreed to take care of her while the others were occupied with Lyric.

Suddenly Omega gets tossed into the side of Thomas as Lyric roars.

"I'VE HAD ENOUGH! WAIT WHAT? YOU FREED THEM? ARGH! I'LL JUST FINISH YOU ALL OFF MYSELF!" Lyric growled.

"BRING IT YOU SPINELESS FREAK!" Sonic shouted.

Lyric angrily slammed his hands on the ground causing a small shockwave sending the engines reeling back. Lyric then summoned more robots that Metal and Omega worked together to take out. Sonic and Knuckles started to fight Lyric by attacking him all over. Lyric swiped at them with his claws or punched them but they would dodge his attacks.

"Had enough snake-breath?" Sonic smirked.

"RRRRRRAAAAAAWWWWWWWWWRRRRRR! I'LL GRIND YOU ALL TO DUST!" Lyric roared.

He shot some electricity from his hands and knocked Sonic and Knuckles back. The Wisps decided to act just as Lyric turned on Thomas with a death glare.

"YOU'RE MINE!" Lyric shouted.

As he charged, Thomas smirked.

SPIKES!

Thomas turns into a large pink spikeball and knocks Lyric back hard. He rams into the central console and part of the Island is turned back to normal. Lyric switches and goes for Percy but gets another surprise.

LAZER!

Percy turns a giant lazer ball and rams into Lyric knocking him back again, the console is hit and the Island is down to 20% of pure metal.

DRILL!

Toby transforms into a drill and zooms all over the place destroying the area.

"NO! I WILL NOT LOSE!" Lyric picked himself up.

"Wanna bet?" Sonic smirked.

"Hey Sonic, how about we do our old Team Blast just for old times sake?" Tails said.

"Great Idea." Sonic said.

And so Knuckles grabbed and them swirled them around and threw them up, Tails kicked Sonic up and away he went.

"BLAST AWAY!"

Sonic went all over the place hitting Lyric so many time that the snake couldn't focus on what was happening. When Sonic finished it, Lyric was slithering around in a daze.

"Ugh...my head." Lyric groaned.

"Give up now Lyric." Sonic said.

Lyric had enough, he shot tons of electricity at Percy, Toby and the Wisps. Sonic, Knuckles, Tails, Omega and Metal jumped at Lyric but they were swatted away. All that was left was Thomas.

"YOU ROTTEN LITTLE ENGINE! YOU'RE RUINING EVERYTHING! YOU THINK YOU'RE SO SPECIAL BUT YOU'RE NOT! PLUS YOU'RE NOTHING BUT A LITTLE ENGINE, YOU'RE WRONG, LITTLE ENGINE CANNOT DO BIG THINGS! YOU JUST GET LUCKY!" Lyric stormed over to him.

He grabbed Thomas' sides with his claws and stared at him with malice in his eyes.

"YOU'RE...ARE...NOTHING..." Lyric growled.

But Thomas only shut his eyes, tears starting to flow down. But he concentrated...and suddenly, the chaos emeralds surrounded him knocking lyric back.

"WHAT?" Lyric gasped.

The others took notice of this as well and smiled. As the emeralds absorbed Thomas...a large flash of light engulfed everyone, and when it died down, they saw that Thomas was Super Thomas again.

"Whoa, he really can do that!" Knuckles said.

Percy, Toby and Sir Topham Hatt were in shock at what they were seeing.

"Thomas...how did you..." Percy trailed off.

Lyric looked a little nervous not knowing what Thomas was going to do. Thomas just stared at him angrily.

"Woah now Thomas...we can talk this out can't we?" Lyric asked nervously.

"CHAOS BLAST!"

Thomas's cab unleashed a large wave of energy that blew up everything around them except his friends and Lyric. The main console of course being one of the things destroyed and the whole Island and returned back to normal, all the buildings, towers and machines crumbled and blew up. The Smelter's was in need or repairs again, but it was kinda back to normal.

"NNNNOOOOOO!" Lyric yelled.

Suddenly Thomas rams straight into him and he pushes him into the Smelters'. Lyric claws against Thomas' sides out of desperation to stop him. He saw they were getting close to the edge where down below was the melting pit.

"NO! NO! STOP!" Lyric yelled.

Suddenly Thomas stopped right on a dime and Lyric went flying back to the edge. The damage to his armor rendered him unable to fly and he dug his claws into the ground. He looked down to see the melting pit below, like it was welcoming him. He looked back up at Thomas who just looked at him with a blank face.

"THOMAS PLEASE! DON'T DO THIS! PLEASE! I'M ACTUALLY BEGGING YOU! PLEASE THOMAS!" Lyric yelled at him.

Thomas shut his eyes and Lyric thought he was going to making his grip loosen instead he heard something.

"Grab on."

Lyric looked to see what looked like a rope made out of energy in front of him. Lyric quickly grabbed it and Thomas pulled him back up to safety. He saw that everyone was there now glaring at him. Lyric fumbled with his words just as Sir Topham Hatt came up to him.

"Listen Lyric, this is MY railway! And I will NOT have it harmed ANY LONGER!" STH said sternly.

STH had a look that would make even Dark Gaia cringe. Lyric lowered his head in embarrassment, his plan failed...all thanks to a little tank engine. Thomas reverted back to normal and Sonic took the emeralds.

"Now unless you want another beatdown, you'll leave this island and never come back!" Sonic said.

Lyric looked back at Thomas who said nothing, he looked at Percy who looked away.

"Fine...I'll go...you'll see me again Sonic the Hedgehog...and to you Thomas...thank you for sparing me."

With that Lyric pressed the button on his chest and he teleported to parts unknown. Sonic patted Thomas on the side.

"Nice job Thomas." Sonic said.

"Thanks Sonic." Thomas smiled.

Back at Tidmouth Sheds, Sir Topham Hatt needed to speak.

"Engines, Mobains and Wisps, and thank you all for your bravery and determination to stop Lyric at all costs. To me engines, you are all really useful!"

The engines all whistled and Toby run his bell. Annie, Clarabel and Henrietta cheered.

"And to you Mobians and Wisps, you are all very brave and strong heroes."

"Thanks sir, that means a lot!" Tails said.

"Ah, it was all Thomas' doing! That guy is powerful!" Knuckles said.

"And very sweet and kind." Shade said.

"I say this calls for a celebration." Sonic said.

The Wisps agreed. And so Sonic, Tails and Knuckles went back to grab some stuff for the party and invited some others including Amy, Blaze, Marine, Cream, Rouge, Big, Silver and the Chaotix...Shadow of course had other things to do. Metal and Omega stayed and talked with the engines. Tails made sure to patch up Shade who was pleased. Sonic privately talked with Thomas.

"We really do make quite a team don't we Thomas?" Sonic said.

"You bet we do! We're unstoppable together." Thomas said.

"Heh, you and your friends are definitely part of our team, and those G.U.N. soldiers should be coming soon. Just remember, if you're ever feeling speedy, you'll know where to find me." Sonic said.

"Heh, well if you ever feeling like traveling and looking for a good place to relax, you'll know where to find me!" Thomas said.

"Right on, by the way you were right!"

"About what?"

"Little engines CAN do big things."

"Thanks Sonic...thanks for believing in me."

 _ **THE END!**_

* * *

 ** _And so ends my favorite crossover to make currently! This was a lot of fun and I hoped you all enjoyed it too! I couldn't really pick an ARC that was my favorite to write because I thought they were all too good to pick!_**

 ** _I have created a sequel called Sonic Chronicles: Dark Island so don't forget to check that out if ya want! Anyways until next time, KINGSTRIKER OUT!_**


End file.
